EcoliWiki - User contributions [en]

ychE 2:Quickview

2008-08-26T16:11:01Z

Tconway: /* Notes */

ychE 2:Quickview

2008-08-26T16:09:26Z

Tconway: Table edited by Tconway via TableEdit

ychE 2:Gene

2008-08-26T16:01:40Z

Tconway: Table edited by Tconway via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ychE_2}}{{Tab On|Gene|ychE_2}}{{Tab|Gene Product(s)|ychE_2}}{{Tab|Expression|ychE_2}}{{Tab|Evolution|ychE_2}}{{Tab|On One Page|ychE_2}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"

|-
!align=left {{table_heading_style}} |Standard name
||
''yhcE''
|-
!align=left {{table_heading_style}} |Mnemonic
||

|-
!align=left {{table_heading_style}} |Synonyms
||
''ECK3207, b3217, JW3184, b4549, JW3187, b4569, JW3184+JW3187''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.T46a9f07ab6411&page=16989&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===
b4569 = yhcE
NOT ychE_2
It appears a transposition occurred with the c and h in yhcE.

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='144168'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
72.49 minutes 
|
MG1655: 3363207..3363686 {{GBrowseFigureByCoord|3362207|3364686|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3362207..3364686 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3363207..3363686&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3365040..3365519 {{GBrowseFigureByCoord|3364040|3366519|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3364040..3366519 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3365040..3365519&plugin_action=Go FASTA Dump]
|-
|
MG1655
|
72.52 minutes 
|
MG1655: 3364703..3364951 {{GBrowseFigureByCoord|3363703|3365951|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3363703..3365951 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3364703..3364951&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3366536..3366784 {{GBrowseFigureByCoord|3365536|3367784|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3365536..3367784 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3366536..3366784&plugin_action=Go FASTA Dump]
|-
|
MG1655
|
 
|
MG1655: 3363207..3364951 {{GBrowseFigureByCoord|3362207|3365951|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3362207..3365951 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3363207..3364951&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3365040..3366784 {{GBrowseFigureByCoord|3364040|3367784|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3364040..3367784 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3365040..3366784&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.N46a9f07b4507a&page=16989&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144169'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.Y46a9f07e2d7c5&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
''ΔyhcE745::kan''
|

|

|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[[cgscmutation:105128|CGSC:105128]]
|

|-
|
''ΔyhcE746::kan''
|

|

|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[[cgscmutation:105130|CGSC:105130]]
|

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.A46a9f07e75ab5&page=16989&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144171'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|

|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:

Primer 1:

Primer 2:
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.T46a9f07f35001&page=16989&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144172'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10562 EcoCyc:G0-10562]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2662 EchoBASE:EB2662]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3217 EcoliGenExpDB:b3217]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG12811 EcoGene:EG12811]
|

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.N46a9f07fd01be&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='99324'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.Q46a70bea3a234&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

ychE 2:Gene

2008-08-26T15:59:21Z

Tconway: /* Notes */

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ychE_2}}{{Tab On|Gene|ychE_2}}{{Tab|Gene Product(s)|ychE_2}}{{Tab|Expression|ychE_2}}{{Tab|Evolution|ychE_2}}{{Tab|On One Page|ychE_2}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''ychE_2''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''yhcE, ECK3207, b3217, JW3184, b4549, JW3187, b4569, JW3184+JW3187, ychE_1''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.T46a9f07ab6411&page=16989&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===
b4569 = yhcE
NOT ychE_2
It appears a transposition occurred with the c and h in yhcE.

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='144168'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
72.49 minutes 
|
MG1655: 3363207..3363686 {{GBrowseFigureByCoord|3362207|3364686|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3362207..3364686 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3363207..3363686&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3365040..3365519 {{GBrowseFigureByCoord|3364040|3366519|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3364040..3366519 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3365040..3365519&plugin_action=Go FASTA Dump]
|-
|
MG1655
|
72.52 minutes 
|
MG1655: 3364703..3364951 {{GBrowseFigureByCoord|3363703|3365951|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3363703..3365951 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3364703..3364951&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3366536..3366784 {{GBrowseFigureByCoord|3365536|3367784|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3365536..3367784 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3366536..3366784&plugin_action=Go FASTA Dump]
|-
|
MG1655
|
 
|
MG1655: 3363207..3364951 {{GBrowseFigureByCoord|3362207|3365951|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10562 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3362207..3365951 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3363207..3364951&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10562 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 3365040..3366784 {{GBrowseFigureByCoord|3364040|3367784|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3364040..3367784 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3365040..3366784&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.N46a9f07b4507a&page=16989&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144169'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.Y46a9f07e2d7c5&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
''ΔyhcE745::kan''
|

|

|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[[cgscmutation:105128|CGSC:105128]]
|

|-
|
''ΔyhcE746::kan''
|

|

|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[[cgscmutation:105130|CGSC:105130]]
|

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.A46a9f07e75ab5&page=16989&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144171'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|

|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:

Primer 1:

Primer 2:
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.T46a9f07f35001&page=16989&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='144172'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10562 EcoCyc:G0-10562]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2662 EchoBASE:EB2662]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3217 EcoliGenExpDB:b3217]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG12811 EcoGene:EG12811]
|

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.N46a9f07fd01be&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='99324'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16989.Q46a70bea3a234&page=16989&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

Letter to Science about wikifying genome information

2008-04-07T21:06:48Z

Tconway: /* draft */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. While David Lipman’s fears that "It would be chaos." are widely shared, the expertise of GenBank's single staff mycologist is unlikely to be superior to the collective, albeit intermittently applied, expertise of the scientists who might participate in wiki curation, including the 250 signers of the Bidartondo et al. letter. Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki (http://ecoliwiki.net), the community annotation component of the EcoliHub project (http://ecolihub.org) and GONUTS (http://gowiki.tamu.edu), a wiki-based browser and annotation engine for the Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, it's lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to the ongoing discussion of the future of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

===signatures===
*James C. Hu, Texas A&M Univ.
*Michael Gribskov, Purdue University
*Tyrrell Conway, University of Oklahoma Advanced Center for Genome Technology
<references/>

----

GenExpDB

2007-09-07T14:24:34Z

Tconway: /* Display Interfaces */

{{Pagetop}}
[[Category:Databases]]
[[Category:EcoliHub Partner]]
[[Category:E. coli Databases]]
[[Category:Gene Expression Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| [[Tyrrell Conway]], OU
|-
| width='30%' | What:
| E. coli Gene Expression Database
|-
| Where:
| [http://chase.ou.edu/oubcf/index.php {{PAGENAME}}]
|-
| Updates
| Incremental, as site is modified with data and applications
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
The University of Oklahoma Bioinformatics Core hosts the E. coli Gene Expression Database. EcoliGenExpDB was designed from the biologist’s perspective, with a tool box-style, integrated and interactive display interface and a simplified warehouse architecture, for analyzing a large and growing body of over 1200 multiplatform microarray experiments (currently 132 public) and 450 mouse intestinal colonization assays (curently 23 public) for the model organism Escherichia coli.

=Content=
==Microarray Data==
*Membrane (Macro) Array data sets generated on Sigma-GenoSys Ecoli Panorama arrays
*Microarray data generated on glass slides printed with Operon, Inc. E. coli ver. 1.0 oligonucleotide probe set
*Affymetrix data generated on custom E. coli GeneChip designed by Conway Laboratory group
*Affymetrix data generated on commercial E. coli GeneChip
==Mouse intestinal colonization data==
*Generated by the Conway laboratory at OU and Paul Cohen's laboratory at the University of Rhode Island
==E. coli Annotation Data==
*ECOLI_K-12: MG1655: NC_000913.2 GI:49175990
*ECOLI_K-12: MG1655: U00096.2 GI:48994873
*ECOLI_K-12: MG1655: K12_SnapShot
*ECOLI_K-12: MG1655: RegulonDB TF-gene interactions file (http://regulondb.ccg.unam.mx/data/NetWorkSet.txt)
*ECOLI_K-12: W3110: AP009048.1 GI:85674274
**Our K-12 annotation database holds information from all 5 of the listed sources and is unique in combining genetic network information with gene function and biological process information.
*ECOLI_042: OUBCF action: Blasted file EC042.art against K12 MG1655 to get gene name
*ECOLI_CFT073: NC_004431.1 GI:26245917
*ECOLI_EDL933: NC_002655.2 GI:16445223
*ECOLI_HS: NZ_AAJY01000001.1 GI:75194227

=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Display Interfaces==
*Database-wide heatmap display
**Database portal is a query box for gene or list of genes created manually or by operon, regulon, or MultiFun process (query history is recorded) (http://chase.ou.edu/oubcf/ecoli/searchlink.php?query="gene_name or b_number or synonym or genome coordinate)
***User defined blue/yellow or red/green color scheme
***User defined wrap or no wrap of heatmap output
**Mouse-over on DB-wide heatmap reveals Gene expression ratio value, Experiment set, and Experiment
**One-click access from DB-wide heatmap to graphic display of individual experiment data: gene expression ratio vs. genome location (http://chase.ou.edu/oubcf/ecoli/searchlink.php?clr=1&dly=0&wrp=1&plt=1&esid=21&eid=193&query="gene_name or b_number#ShowGraph")
***Mouse-over on graph shows gene name and gene expression ratio value
***One-click on graph-data point executes DB-wide heatmap query for for any gene in graphic display
***User defined significance values shown on graph
***Displays lists of up-regulated and down-regulated genes
**One-click access from DB-wide heatmap to overlay on E. coli metabolic pathway chart in Omics Viewer (Biocyc Pathway Tools 9.0 running locally) (http://chase.ou.edu/ouma/omics/"filename".html
**Genome browser line shows genome location and neighboring genes (clickable for DB-wide heatmap query)
**Annotation line shows information in local annotation database for queried gene(s)
***Select information from local annotation database
***Select metalinks to external sites listed below
***Select gene-specific query of Mouse Colonization Data
*'''E'''xpression-'''Ring''' displays Gene expression ration data in a blue/yellow heat map of concentric rings, one for each experiment, with all displayed Transcription Factor (TF) genes labeled on outside ring(s) and with hyperbolas connecting to all target genes regulated by each TF
**Mouse-over on data rings displays Experiment_name, Gene_name, Locus_tag, LogRatio (expression value), Operon, Regulated by, and position on the ring
**Select ''Data'' to choose datasets to be loaded into E-Ring display
***Select ''User Data'' to upload Data file, and/or Regulator file, and/or Gene information file
***Select ''OUBCF Data'' to load local data from lists of Experiments and Experiment sets
display a list of all TF genes in the display, with check boxes to select/deselect TFs and hyperbola connecting lines for display on redraw
**Select ''Filter'' for redrawing display by user defined criteria:
***Select ''Genes'' to filter data by "expression" (fold-changes, standard deviation value) or "Function" (MultiFun process) or "Regulon" for chosen experiment(s)
***Select ''Connections'' to filter data by list of all TF genes in the display, with check boxes to select/deselect TFs and hyperbola connecting lines for display on redraw
***Select ''Order'' to reorder genes in display by hierarchical clustering
**Select ''Info'' to display information about the data in the display
**Select "Options" to change the display graphics properties
**Select ''Stats'' to access popup window containing regulatory information in display:
***All TFs in display
***The number of target genes regulated by that TF
****Click on ''Number of regulated genes'' to access popup window displaying blue/yellow heatmap of all genes in operon/regulon and lists of TFs that regulate each gene
***For each experiment ring, the average log expression ratio value for all target genes in the operon/regulon
***A list of all other regulators that control genes regulated by that TF
**A ''Gene'' query box accesses a popup window to indicate location of gene(s) on data rings
*Browse Experiment sets
**Select ''Experiment'' to access tab-delimited data and array information
**Select ''Cluster'' to display hierarchical clustered data in heatmap
**Select ''Heatmap'' tp display experiment set data ordered by genome location
**Select ''Genome'' to display experiment set data in concentric rings for each time point
**Select ''Time Series'' for graphic display of experiment set data (optimized for time series data)
***User defined display of genes selected from lists (soon to include operons, regulons, biological processes)
***User defined selection of experiments to be displayed from experiments set
**Select ''Experiment Design'' for biological protocols and publication information

==Usage examples==

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
A DB-specific article has not yet been published. 
Several papers published by the Conway laboratory reference data in EcoliGenExpDB, including: 
*Traxler, M. F., D.-E. Chang, and T. Conway. 2006. Guanosine 5’,3’-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli. Proc. Nat. Acad. Sci. 103: 2374-2379. 
*Chang, D.E., D. Smalley, D. L. Tucker, M. P. Leatham, W. E. Norris, S. J. Stevenson, A. B. Anderson, J. E. Grissom, D. C. Laux, P. S. Cohen, and T. Conway. Carbon nutrition of Escherichia coli in the mouse intestine. 2004. Proc. Nat. Acad. Sci. 101: 7427–7432.
<references/>

=External Links=
[http://chase.ou.edu/oubcf/index.php {{PAGENAME}}]
==Metalinks from external sites to microarray data at EcoliGenExpDB ==
Using syntax http://chase.ou.edu/oubcf/ecoli/searchlink.php?bnum="b_number"
*EcoCyc
*EcoGene
*PIR (Protein Information Resouce)
*RegulonDB

==Links out==
*ASAP
*ColiBase
*Colibri
*EchoBase
*EcoCyc
*EcoGene
*GenoBase
*Gene Ontology
*KEGG
*NCBI
*RegulonDB
*SwissProt

==Discussion of {{PAGENAME}} on other websites==

Database Overview

2006-08-15T23:29:42Z

Tconway: /* Experimental data */

[[Category:Databases]]
''See also'' [[List of Databases]]
{{RightTOC}}
=Content & Features at different databases=
These sections list information we want...add text to indicate where the information can be found.
==Genomes==
DNA sequences for complete and partial genomes are mostly at Genbank.
===''E. coli''===
{|{{Prettytable}}
|-
! Strain || Genbank Accession || Other Sources || Notes
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=115 MG1655]
| Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=NC_000913 NC_000913]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=U00096 U00096]
|
|Complete genome
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19221 W3110]
|Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AC_000091 AC_000091]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AP009048 AP009048]
|
|Complete genome
|}
===Phage===

===Plasmids===
These should include F and F's (see Ch 129 of the E. coli Book)

==Genetics==
===Genes===
We use gene and locus interchangeably, but gene is perhaps a subset of locus (see [[Talk:Database_Overview|Discussion page]]).
Note that some customization will be needed for phage and plasmid genes vs. chromosomal genes.
====Nomenclature====
See also [[Help:Genetic_nomenclature]]
*Standard name: e.g. ''lacZ'', or ''rpoD''
*Synonyms: e.g. ''groP'' for ''dnaK'', ''alt'' for ''rpoD''
*Accessions
**To genomic sequence (bnum, JW, ECK)
**To external databases (GenBank, Swissprot, ASAP, EcoCyc, etc.)
History and references for the above, e.g. "lac for lactose metabolism (ref)"

====Gene Sequence====
**-10 signal
**-35 signal
**5' UTR
**3' UTR
**5' End of Message
**''att'' sites
**Anti-terminator
**Attenuator
**CDS
**D-loop
**Enhancer
**Gene
**Intron and exon
**modified base
**mRNA
**nut sites
**operator
**operon
**''ori''C
**''ori''T
**Precursor RNA
**Primer Bind
**Promoter
**Protein Binding
**RBS
**Replication origin
**Repeat Region
**rRNA
**'shifty' sequences
**stem loop
**terminator (Rho dependent and independent)
**translation start codon
**transcriptional start site
**tRNA

====Gene models====
A gene model defines where a gene is on the genomic DNA. Different annotators may disagree about where a gene starts and stops.
Need to look at Sequence Ontology features

===Map information===
*Location in map units
*Cotransduction frequencies to nearby markers
*Presence or absence in different strains
**Covered by deletions
**Covered by F's
**Hfr to transfer
**Covered by ASKA clones
**Covered by Kohara phage
**Covered by Clark-Carbon clone
References and commentary

===Alleles===
Mutant alleles and links to strains containing these and references.

===Phenotypes===
Phenotypes for knockout and other alleles. Phenotypes should be annotated to a phenotype ontology to aid comparison among genes. Discussions have begun with SGD on a shared microbial phenotype ontology.

==Gene Products==
===Proteins===
====Nomenclature====
*Protein Name - just gene product notation e.g. DnaK. (this will be pagename in wiki)
**Protein name synonyms
*Product description/name - e.g. Hsp70-family chaperone
**Protein family (pfam, Interpro)
**NCBI
**From Uniprot
**Other synonyms
*Accessions/IDs/Crossrefs
**Protein genbank ID (gi)
**Uniprot/Swissprot/TrEmbl
**Systematic gene name (EcoliHub ID)
**Genome ID# (bnum JW ECK)
*Source (organism, strain, substrain)

====Sequence====
*Protein seqence/length
*Annotation Version (Reference)
*Codon adaptation index
*Sequence features
**Domains/Motifs (Interpro, Pfam, CDD)
**Signal sequences
**Other localization/post-translational modification motifs
References

====Physical Properties====
*Calculated molecular weight/PI
*Observed molecular weight/PI
*Calculated extinction coefficient

====Protein Structure====
*Structure (PDB)
*Predicted
**structure
**coiled coils
**other motifs
**transmembrane segments/topology
*Structure families (SCOP,CATH)

====Protein Function====
*Function (GO has refs)
*Enzyme activity EC number (add refs) - look at BRENDA
*Pathway/process links
*Ligands
*Regulation (allosteric/feedback)
*Interactions

====Experimental Data====
*Proteomics study
*Protein-protein interaction
*Purification
*Antibody
*Localization

====Evolutionary relationships====
*BLAST/FASTA/Homolog listing
*Orthologous groups (COG)
*Taxonomic distribution
**Origin (horizontal vs vertical)
*Ortholog lists (by whatever method)

===RNAs===
===DNA elements===
==Operons==
==Regulons==
==Mobile Genetic Elements==
===Prophages===
===IS elements and Transposons===
===Plasmids===
==Experimental data==
===Expression===
*Microarrays
*Proteomics
**2-D gels protein levels
**Mass Spec
***protein levels
***protein modification
*Metabolomics
*Growth curves
*Gene reporter fusions
===Localization===
*GFP-fusions
===Interactions===
===Ecology===
*Mouse colonization fitness assays

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
*[[ASAP]] (participant of the NAR 06 paper) enter query as feature name from [https://asap.ahabs.wisc.edu/asap/query_features.php?LocationID=WIS&SequenceVersionID=42 query page] (link is to MG1655; other genomes available) returns page with link to features page.
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)

| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (linked to COG)
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to GenBank)
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to PDB)
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (Linked to EcoGene)
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to CGSC)
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-08-15T23:28:31Z

Tconway: /* Experimental data */

[[Category:Databases]]
''See also'' [[List of Databases]]
{{RightTOC}}
=Content & Features at different databases=
These sections list information we want...add text to indicate where the information can be found.
==Genomes==
DNA sequences for complete and partial genomes are mostly at Genbank.
===''E. coli''===
{|{{Prettytable}}
|-
! Strain || Genbank Accession || Other Sources || Notes
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=115 MG1655]
| Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=NC_000913 NC_000913]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=U00096 U00096]
|
|Complete genome
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19221 W3110]
|Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AC_000091 AC_000091]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AP009048 AP009048]
|
|Complete genome
|}
===Phage===

===Plasmids===
These should include F and F's (see Ch 129 of the E. coli Book)

==Genetics==
===Genes===
We use gene and locus interchangeably, but gene is perhaps a subset of locus (see [[Talk:Database_Overview|Discussion page]]).
Note that some customization will be needed for phage and plasmid genes vs. chromosomal genes.
====Nomenclature====
See also [[Help:Genetic_nomenclature]]
*Standard name: e.g. ''lacZ'', or ''rpoD''
*Synonyms: e.g. ''groP'' for ''dnaK'', ''alt'' for ''rpoD''
*Accessions
**To genomic sequence (bnum, JW, ECK)
**To external databases (GenBank, Swissprot, ASAP, EcoCyc, etc.)
History and references for the above, e.g. "lac for lactose metabolism (ref)"

====Gene Sequence====
**-10 signal
**-35 signal
**5' UTR
**3' UTR
**5' End of Message
**''att'' sites
**Anti-terminator
**Attenuator
**CDS
**D-loop
**Enhancer
**Gene
**Intron and exon
**modified base
**mRNA
**nut sites
**operator
**operon
**''ori''C
**''ori''T
**Precursor RNA
**Primer Bind
**Promoter
**Protein Binding
**RBS
**Replication origin
**Repeat Region
**rRNA
**'shifty' sequences
**stem loop
**terminator (Rho dependent and independent)
**translation start codon
**transcriptional start site
**tRNA

====Gene models====
A gene model defines where a gene is on the genomic DNA. Different annotators may disagree about where a gene starts and stops.
Need to look at Sequence Ontology features

===Map information===
*Location in map units
*Cotransduction frequencies to nearby markers
*Presence or absence in different strains
**Covered by deletions
**Covered by F's
**Hfr to transfer
**Covered by ASKA clones
**Covered by Kohara phage
**Covered by Clark-Carbon clone
References and commentary

===Alleles===
Mutant alleles and links to strains containing these and references.

===Phenotypes===
Phenotypes for knockout and other alleles. Phenotypes should be annotated to a phenotype ontology to aid comparison among genes. Discussions have begun with SGD on a shared microbial phenotype ontology.

==Gene Products==
===Proteins===
====Nomenclature====
*Protein Name - just gene product notation e.g. DnaK. (this will be pagename in wiki)
**Protein name synonyms
*Product description/name - e.g. Hsp70-family chaperone
**Protein family (pfam, Interpro)
**NCBI
**From Uniprot
**Other synonyms
*Accessions/IDs/Crossrefs
**Protein genbank ID (gi)
**Uniprot/Swissprot/TrEmbl
**Systematic gene name (EcoliHub ID)
**Genome ID# (bnum JW ECK)
*Source (organism, strain, substrain)

====Sequence====
*Protein seqence/length
*Annotation Version (Reference)
*Codon adaptation index
*Sequence features
**Domains/Motifs (Interpro, Pfam, CDD)
**Signal sequences
**Other localization/post-translational modification motifs
References

====Physical Properties====
*Calculated molecular weight/PI
*Observed molecular weight/PI
*Calculated extinction coefficient

====Protein Structure====
*Structure (PDB)
*Predicted
**structure
**coiled coils
**other motifs
**transmembrane segments/topology
*Structure families (SCOP,CATH)

====Protein Function====
*Function (GO has refs)
*Enzyme activity EC number (add refs) - look at BRENDA
*Pathway/process links
*Ligands
*Regulation (allosteric/feedback)
*Interactions

====Experimental Data====
*Proteomics study
*Protein-protein interaction
*Purification
*Antibody
*Localization

====Evolutionary relationships====
*BLAST/FASTA/Homolog listing
*Orthologous groups (COG)
*Taxonomic distribution
**Origin (horizontal vs vertical)
*Ortholog lists (by whatever method)

===RNAs===
===DNA elements===
==Operons==
==Regulons==
==Mobile Genetic Elements==
===Prophages===
===IS elements and Transposons===
===Plasmids===
==Experimental data==
===Expression===
*Microarrays
*Proteomics
**2-D gels protein levels
**Mass Spec
***protein levels
***protein modification
*Metabolomics
*Growth curves
===Localization===
===Interactions===
===Ecology===
*Mouse colonization fitness assays

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
*[[ASAP]] (participant of the NAR 06 paper) enter query as feature name from [https://asap.ahabs.wisc.edu/asap/query_features.php?LocationID=WIS&SequenceVersionID=42 query page] (link is to MG1655; other genomes available) returns page with link to features page.
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)

| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (linked to COG)
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to GenBank)
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to PDB)
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (Linked to EcoGene)
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to CGSC)
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-08-15T21:56:37Z

Tconway: /* Expression */

[[Category:Databases]]
''See also'' [[List of Databases]]
{{RightTOC}}
=Content & Features at different databases=
These sections list information we want...add text to indicate where the information can be found.
==Genomes==
DNA sequences for complete and partial genomes are mostly at Genbank.
===''E. coli''===
{|{{Prettytable}}
|-
! Strain || Genbank Accession || Other Sources || Notes
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=115 MG1655]
| Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=NC_000913 NC_000913]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=U00096 U00096]
|
|Complete genome
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19221 W3110]
|Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AC_000091 AC_000091]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AP009048 AP009048]
|
|Complete genome
|}
===Phage===

===Plasmids===
These should include F and F's (see Ch 129 of the E. coli Book)

==Genetics==
===Genes===
We use gene and locus interchangeably, but gene is perhaps a subset of locus (see [[Talk:Database_Overview|Discussion page]]).
Note that some customization will be needed for phage and plasmid genes vs. chromosomal genes.
====Nomenclature====
See also [[Help:Genetic_nomenclature]]
*Standard name: e.g. ''lacZ'', or ''rpoD''
*Synonyms: e.g. ''groP'' for ''dnaK'', ''alt'' for ''rpoD''
*Accessions
**To genomic sequence (bnum, JW, ECK)
**To external databases (GenBank, Swissprot, ASAP, EcoCyc, etc.)
History and references for the above, e.g. "lac for lactose metabolism (ref)"

====Gene Sequence====
**-10 signal
**-35 signal
**5' UTR
**3' UTR
**5' End of Message
**''att'' sites
**Anti-terminator
**Attenuator
**CDS
**D-loop
**Enhancer
**Gene
**Intron and exon
**modified base
**mRNA
**nut sites
**operator
**operon
**''ori''C
**''ori''T
**Precursor RNA
**Primer Bind
**Promoter
**Protein Binding
**RBS
**Replication origin
**Repeat Region
**rRNA
**'shifty' sequences
**stem loop
**terminator (Rho dependent and independent)
**translation start codon
**transcriptional start site
**tRNA

====Gene models====
A gene model defines where a gene is on the genomic DNA. Different annotators may disagree about where a gene starts and stops.
Need to look at Sequence Ontology features

===Map information===
*Location in map units
*Cotransduction frequencies to nearby markers
*Presence or absence in different strains
**Covered by deletions
**Covered by F's
**Hfr to transfer
**Covered by AKSA clones
**Covered by Kohara phage
**Covered by Clark-Carbon clone
References and commentary

===Alleles===
Mutant alleles and links to strains containing these and references.

===Phenotypes===
Phenotypes for knockout and other alleles. Phenotypes should be annotated to a phenotype ontology to aid comparison among genes. Discussions have begun with SGD on a shared microbial phenotype ontology.

==Gene Products==
===Proteins===
====Nomenclature====
*Protein Name - just gene product notation e.g. DnaK. (this will be pagename in wiki)
**Protein name synonyms
*Product description/name - e.g. Hsp70-family chaperone
**Protein family (pfam, Interpro)
**NCBI
**From Uniprot
**Other synonyms
*Accessions/IDs/Crossrefs
**Protein genbank ID (gi)
**Uniprot/Swissprot/TrEmbl
**Systematic gene name (EcoliHub ID)
**Genome ID# (bnum JW ECK)
*Source (organism, strain, substrain)

====Sequence====
*Protein seqence/length
*Annotation Version (Reference)
*Codon adaptation index
*Sequence features
**Domains/Motifs (Interpro, Pfam, CDD)
**Signal sequences
**Other localization/post-translational modification motifs
References

====Physical Properties====
*Calculated molecular weight/PI
*Observed molecular weight/PI
*Calculated extinction coefficient

====Protein Structure====
*Structure (PDB)
*Predicted
**structure
**coiled coils
**other motifs
**transmembrane segments/topology
*Structure families (SCOP,CATH)

====Protein Function====
*Function (GO has refs)
*Enzyme activity EC number (add refs) - look at BRENDA
*Pathway/process links
*Ligands
*Regulation (allosteric/feedback)
*Interactions

====Experimental Data====
*Proteomics study
*Protein-protein interaction
*Purification
*Antibody
*Localization

====Evolutionary relationships====
*BLAST/FASTA/Homolog listing
*Orthologous groups (COG)
*Taxonomic distribution
**Origin (horizontal vs vertical)
*Ortholog lists (by whatever method)

===RNAs===
===DNA elements===
==Operons==
==Regulons==
==Mobile Genetic Elements==
===Prophages===
===IS elements and Transposons===
===Plasmids===
==Experimental data==
===Expression===
*Microarrays
*Proteomics
**2-D gels protein levels
**Mass Spec
***protein levels
***protein modification

===Localization===
===Interactions===
===Ecology===
*Mouse colonization fitness assays

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
*[[ASAP]] (participant of the NAR 06 paper) enter query as feature name from [https://asap.ahabs.wisc.edu/asap/query_features.php?LocationID=WIS&SequenceVersionID=42 query page] (link is to MG1655; other genomes available) returns page with link to features page.
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)

| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (linked to COG)
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to GenBank)
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to PDB)
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (Linked to EcoGene)
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to CGSC)
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

Database Overview

2006-08-15T21:54:32Z

Tconway: /* Experimental data */

[[Category:Databases]]
''See also'' [[List of Databases]]
{{RightTOC}}
=Content & Features at different databases=
These sections list information we want...add text to indicate where the information can be found.
==Genomes==
DNA sequences for complete and partial genomes are mostly at Genbank.
===''E. coli''===
{|{{Prettytable}}
|-
! Strain || Genbank Accession || Other Sources || Notes
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=115 MG1655]
| Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=NC_000913 NC_000913]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=U00096 U00096]
|
|Complete genome
|-
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genome&cmd=Retrieve&dopt=Overview&list_uids=19221 W3110]
|Refseq: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AC_000091 AC_000091]
GenBank: [http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi??db=nucleotide&val=AP009048 AP009048]
|
|Complete genome
|}
===Phage===

===Plasmids===
These should include F and F's (see Ch 129 of the E. coli Book)

==Genetics==
===Genes===
We use gene and locus interchangeably, but gene is perhaps a subset of locus (see [[Talk:Database_Overview|Discussion page]]).
Note that some customization will be needed for phage and plasmid genes vs. chromosomal genes.
====Nomenclature====
See also [[Help:Genetic_nomenclature]]
*Standard name: e.g. ''lacZ'', or ''rpoD''
*Synonyms: e.g. ''groP'' for ''dnaK'', ''alt'' for ''rpoD''
*Accessions
**To genomic sequence (bnum, JW, ECK)
**To external databases (GenBank, Swissprot, ASAP, EcoCyc, etc.)
History and references for the above, e.g. "lac for lactose metabolism (ref)"

====Gene Sequence====
**-10 signal
**-35 signal
**5' UTR
**3' UTR
**5' End of Message
**''att'' sites
**Anti-terminator
**Attenuator
**CDS
**D-loop
**Enhancer
**Gene
**Intron and exon
**modified base
**mRNA
**nut sites
**operator
**operon
**''ori''C
**''ori''T
**Precursor RNA
**Primer Bind
**Promoter
**Protein Binding
**RBS
**Replication origin
**Repeat Region
**rRNA
**'shifty' sequences
**stem loop
**terminator (Rho dependent and independent)
**translation start codon
**transcriptional start site
**tRNA

====Gene models====
A gene model defines where a gene is on the genomic DNA. Different annotators may disagree about where a gene starts and stops.
Need to look at Sequence Ontology features

===Map information===
*Location in map units
*Cotransduction frequencies to nearby markers
*Presence or absence in different strains
**Covered by deletions
**Covered by F's
**Hfr to transfer
**Covered by AKSA clones
**Covered by Kohara phage
**Covered by Clark-Carbon clone
References and commentary

===Alleles===
Mutant alleles and links to strains containing these and references.

===Phenotypes===
Phenotypes for knockout and other alleles. Phenotypes should be annotated to a phenotype ontology to aid comparison among genes. Discussions have begun with SGD on a shared microbial phenotype ontology.

==Gene Products==
===Proteins===
====Nomenclature====
*Protein Name - just gene product notation e.g. DnaK. (this will be pagename in wiki)
**Protein name synonyms
*Product description/name - e.g. Hsp70-family chaperone
**Protein family (pfam, Interpro)
**NCBI
**From Uniprot
**Other synonyms
*Accessions/IDs/Crossrefs
**Protein genbank ID (gi)
**Uniprot/Swissprot/TrEmbl
**Systematic gene name (EcoliHub ID)
**Genome ID# (bnum JW ECK)
*Source (organism, strain, substrain)

====Sequence====
*Protein seqence/length
*Annotation Version (Reference)
*Codon adaptation index
*Sequence features
**Domains/Motifs (Interpro, Pfam, CDD)
**Signal sequences
**Other localization/post-translational modification motifs
References

====Physical Properties====
*Calculated molecular weight/PI
*Observed molecular weight/PI
*Calculated extinction coefficient

====Protein Structure====
*Structure (PDB)
*Predicted
**structure
**coiled coils
**other motifs
**transmembrane segments/topology
*Structure families (SCOP,CATH)

====Protein Function====
*Function (GO has refs)
*Enzyme activity EC number (add refs) - look at BRENDA
*Pathway/process links
*Ligands
*Regulation (allosteric/feedback)
*Interactions

====Experimental Data====
*Proteomics study
*Protein-protein interaction
*Purification
*Antibody
*Localization

====Evolutionary relationships====
*BLAST/FASTA/Homolog listing
*Orthologous groups (COG)
*Taxonomic distribution
**Origin (horizontal vs vertical)
*Ortholog lists (by whatever method)

===RNAs===
===DNA elements===
==Operons==
==Regulons==
==Mobile Genetic Elements==
===Prophages===
===IS elements and Transposons===
===Plasmids===
==Experimental data==
===Expression===
===Localization===
===Interactions===
===Ecology===
*Mouse colonization fitness assays

=Query types=
==Query by gene name==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3'|gene name (e.g. lacY)
*[[ASAP]] (participant of the NAR 06 paper) enter query as feature name from [https://asap.ahabs.wisc.edu/asap/query_features.php?LocationID=WIS&SequenceVersionID=42 query page] (link is to MG1655; other genomes available) returns page with link to features page.
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)

| sequence
|
*[[ASAP]] (participant of the NAR 06 paper)
*[[GenoBase]] (participant of the NAR 06 paper)
*[[EcoCyc]] (participant of the NAR 06 paper)
*[[EcoGene]] (participant of the NAR 06 paper)
*[[RegulonDB]] (?)
*[[KEGG]]: AA and nucleotide sequences (imported from Genbank)
|-
|description 
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation)
|-
|
function 
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (linked to COG)
*[[EcoCyc]]
*[[EcoGene]]: Included in Description
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
localization 
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
|
process (GO definitions ) 
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: (no result)

|-
| rowspan ='4'|
gene name (namespace1)
|
gene name (namespace2) 
Some namespaces:
|-
|
*genbank ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to GenBank)
*[[RegulonDB]]
*[[KEGG]]: yes + link to GenBank
|-
|
*pdb ID
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to PDB)
*[[RegulonDB]]
*[[KEGG]]: id not explicitly shown, but link to PDB
|-
|
*ecogene ID
|
*[[ASAP]]
*[[GenoBase]]: Indirectly (Linked to EcoGene)
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: no
|-
|gene name
|pathway
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to AmiGO)
*[[RegulonDB]]
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry
|-
| rowspan='3'|gene name
|experimental data
|-
|
*gene expression
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*protein interaction
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|gene name (species 1)
|gene name( species 2)
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes

|-
| rowspan='3'|gene name
|
*mutations
|
*[[ASAP]]
*[[GenoBase]]: Included in Experimental Data
*[[EcoCyc]]
*[[EcoGene]]: Indirectly (Linked to CGSC)
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*sequence difference
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*phenotype
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by pathway==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|pathway
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries
|-
| rowspan ='2' |metabolic process
|
*regulatory circuits
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
|-
|
*transcription factors/sites
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by DNA location or sequence==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|DNA location
|Gene name
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|sequence
|related sequence (BLAST)
|
*[[ASAP]]
*[[GenoBase]]: Yes
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by Function==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
|gene function (GO term) 
same for process and other GO branches
|gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: Yes
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

==Query by strain==
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
| '''How this is handled in different databases'''
|-
| rowspan = '3' |strain ID
|
*gene name
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*mutation
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|-
|
*source
|
*[[ASAP]]
*[[GenoBase]]: No
*[[EcoCyc]]
*[[EcoGene]]: No
*[[RegulonDB]]
*[[KEGG]]: (no result)
|}

ECCE

2006-07-10T20:49:02Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Michael Ehrmann
|-
| width='30%' | What:
| ''E. coli Cell Envelope Proteins''
|-
| Where:
| School of Biosciences, Cardiff University
[http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/ecce.htm {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
ECCE is a functional classification of cell envelope proteins.
[http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/ecce.htm {{PAGENAME}}] is...
=Content=
*Topology predictions are shown for cytoplasmic membrane proteins.
*A list of 452 signal sequences of E. coli cell envelope proteins
*A link to a list of Tat signal sequences provided by Tracy Palmer
*Periplasmic proteins listed according to their size
*Outer membrane proteins listed according to their size
=Using {{PAGENAME}}=
==Browsing==
Browse by:
*Integral membrane protein
*Periplasmic protein
*Outer membrane protein
*Lists of genes as described in context
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/ecce.htm {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

ECCE

2006-07-10T20:48:03Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Michael Ehrmann
|-
| width='30%' | What:
| ''E. coli Cell Envelope Proteins''
|-
| Where:
| School of Biosciences, Cardiff University
[http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/ecce.htm {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
ECCE is a functional classification of cell envelope proteins.
[http://ASAP {{PAGENAME}}] is...
=Content=
*Topology predictions are shown for cytoplasmic membrane proteins.
*A list of 452 signal sequences of E. coli cell envelope proteins
*A link to a list of Tat signal sequences provided by Tracy Palmer
*Periplasmic proteins listed according to their size

Outer membrane proteins listed according to their size
=Using {{PAGENAME}}=
==Browsing==
Browse by:
*Integral membrane protein
*Periplasmic protein
*Outer membrane protein
*Lists of genes as described in context
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

ECCE

2006-07-10T20:37:44Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://ASAP {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Escherichia coli transcription factor binding sites (TFBS)

2006-07-10T20:34:25Z

Tconway:

'''TFBS'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''L.A. McCue''
|-
| width='30%' | What:
| ''Transcription Factor Binding Sites''
|-
| Where:
| [http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
This site presents transcription factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding. Predictions were made upstream of 2086 E. coli genes; that is, all genes for which: 1) there was at least 50 bp upstream intergenic sequence, and 2) a probable ortholog was identified among the species used for comparison. The gene names and annotations used are those from the E. coli genome GenBank entry (U00096). Where available, correspondence of our predictions with experimentally verified binding sites or known repeats is presented. Regulons have been predicted by clustering these phylogenetic footprinted motifs.
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}] is...
=Content=
The prediction page for each gene contains the following information.
*The genome coordinates, orientation, gene type (CDS or RNA), gene name, EcoGene link, and annotation for the target gene, and also the genes immediately flanking the target gene.
*The genome coordinates, source of information, transcription factor name, and annotation for known TF-binding sites that regulate the target gene.
*A listing of the species for which a probable ortholog of the target gene was identified.
*The predictions made for the target gene, separated into those predictions that were above our cutoff for statistical significance (p < 0.05), and those that were below the cutoff. For each prediction the following information is given: the Average MAP (maximum a posteriori probability) value, the genome coordinates (an "R" indicates that the sequence given is the reverse complement of that in the GenBank entry at those coordinates), the site sequence (plus 5 bp flanking), the transcription factor site type and overlap in bp (if site overlaps a known transcription factor binding site), the repeat name (if site overlaps a known repeat), a sequence logo if the motif model, a sequence logo of the aligned sites, a sequence alignment of the sites. For genes that are divergently transcribed, predictions were made for each gene separately and overlap with known sites is reported for all regulatory sites in that promoter region (sites that regulate the target gene and sites that regulate the divergently transcribed gene).
*The critical MAP values for the target gene calculated for p = 0.01, p = 0.05, p = 0.1, and p = 0.2.
=Using {{PAGENAME}}=
==Browsing==
Browse list of genes
==Searching==
Query by gene name
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
L.A. McCue, W. Thompson, C.S. Carmack, and C.E. Lawrence. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Research, 12: 1523-1532.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=12368244&query_hl=9&itool=pubmed_docsum
=External Links=
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Escherichia coli transcription factor binding sites (TFBS)

2006-07-10T20:32:55Z

Tconway:

'''TFBS'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''L.A. McCue''
|-
| width='30%' | What:
| ''Transcription Factor Binding Sites''
|-
| Where:
| [http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
This site presents transcription factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding. Predictions were made upstream of 2086 E. coli genes; that is, all genes for which: 1) there was at least 50 bp upstream intergenic sequence, and 2) a probable ortholog was identified among the species used for comparison. The gene names and annotations used are those from the E. coli genome GenBank entry (U00096). Where available, correspondence of our predictions with experimentally verified binding sites or known repeats is presented. Regulons have been predicted by clustering these phylogenetic footprinted motifs.
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}] is...
=Content=
The prediction page for each gene contains the following information.
*1) The genome coordinates, orientation, gene type (CDS or RNA), gene name, EcoGene link, and annotation for the target gene, and also the genes immediately flanking the target gene.
*2) The genome coordinates, source of information, transcription factor name, and annotation for known TF-binding sites that regulate the target gene.
*3) A listing of the species for which a probable ortholog of the target gene was identified.
*4) The predictions made for the target gene, separated into those predictions that were above our cutoff for statistical significance (p < 0.05), and those that were below the cutoff. For each prediction the following information is given: the Average MAP (maximum a posteriori probability) value, the genome coordinates (an "R" indicates that the sequence given is the reverse complement of that in the GenBank entry at those coordinates), the site sequence (plus 5 bp flanking), the transcription factor site type and overlap in bp (if site overlaps a known transcription factor binding site), the repeat name (if site overlaps a known repeat), a sequence logo if the motif model, a sequence logo of the aligned sites, a sequence alignment of the sites. For genes that are divergently transcribed, predictions were made for each gene separately and overlap with known sites is reported for all regulatory sites in that promoter region (sites that regulate the target gene and sites that regulate the divergently transcribed gene).
5) The critical MAP values for the target gene calculated for p = 0.01, p = 0.05, p = 0.1, and p = 0.2.
=Using {{PAGENAME}}=
==Browsing==
Browse list of genes
==Searching==
Query by gene name
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
L.A. McCue, W. Thompson, C.S. Carmack, and C.E. Lawrence. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Research, 12: 1523-1532.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=12368244&query_hl=9&itool=pubmed_docsum
=External Links=
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Escherichia coli transcription factor binding sites (TFBS)

2006-07-10T20:32:10Z

Tconway:

'''TFBS'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''L.A. McCue''
|-
| width='30%' | What:
| ''Transcription Factor Binding Sites''
|-
| Where:
| [http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
This site presents transcription factor binding site predictions in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding. Predictions were made upstream of 2086 E. coli genes; that is, all genes for which: 1) there was at least 50 bp upstream intergenic sequence, and 2) a probable ortholog was identified among the species used for comparison. The gene names and annotations used are those from the E. coli genome GenBank entry (U00096). Where available, correspondence of our predictions with experimentally verified binding sites or known repeats is presented. Regulons have been predicted by clustering these phylogenetic footprinted motifs.
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}] is...
=Content=
The prediction page for each gene contains the following information.
1) The genome coordinates, orientation, gene type (CDS or RNA), gene name, EcoGene link, and annotation for the target gene, and also the genes immediately flanking the target gene.
2) The genome coordinates, source of information, transcription factor name, and annotation for known TF-binding sites that regulate the target gene.
3) A listing of the species for which a probable ortholog of the target gene was identified.
4) The predictions made for the target gene, separated into those predictions that were above our cutoff for statistical significance (p < 0.05), and those that were below the cutoff. For each prediction the following information is given: the Average MAP (maximum a posteriori probability) value, the genome coordinates (an "R" indicates that the sequence given is the reverse complement of that in the GenBank entry at those coordinates), the site sequence (plus 5 bp flanking), the transcription factor site type and overlap in bp (if site overlaps a known transcription factor binding site), the repeat name (if site overlaps a known repeat), a sequence logo if the motif model, a sequence logo of the aligned sites, a sequence alignment of the sites. For genes that are divergently transcribed, predictions were made for each gene separately and overlap with known sites is reported for all regulatory sites in that promoter region (sites that regulate the target gene and sites that regulate the divergently transcribed gene).
5) The critical MAP values for the target gene calculated for p = 0.01, p = 0.05, p = 0.1, and p = 0.2.
=Using {{PAGENAME}}=
==Browsing==
Browse list of genes
==Searching==
Query by gene name
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
L.A. McCue, W. Thompson, C.S. Carmack, and C.E. Lawrence. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Research, 12: 1523-1532.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=12368244&query_hl=9&itool=pubmed_docsum
=External Links=
[http://bayesweb.wadsworth.org/binding_sites/index.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

PMTG

2006-07-10T20:11:06Z

Tconway: /* Searching */

'''PMTG'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Jean-Marie Clément''
|-
| width='30%' | What:
| ''Short repeated palindromes in enterobacteria''
|-
| Where:
| Pasteur Institute
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
The Unit of Molecular Programming and Genetic Toxicology (UMPGT) is interested in the organisation, the stability, the evolution and the expression of the genome of gamma proteobacteria. Studies are developing along four main research axes.
*ABC transporters
*BIME for Bacterial Interspersed Mosaic Element
*genotoxic agents
*bacterial super-integrons
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
There does not appear to be a database behind the information presented at this site, which is described as being "under construction".

==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
=External Links=
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

PMTG

2006-07-10T20:10:08Z

Tconway:

'''PMTG'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Jean-Marie Clément''
|-
| width='30%' | What:
| ''Short repeated palindromes in enterobacteria''
|-
| Where:
| Pasteur Institute
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
The Unit of Molecular Programming and Genetic Toxicology (UMPGT) is interested in the organisation, the stability, the evolution and the expression of the genome of gamma proteobacteria. Studies are developing along four main research axes.
*ABC transporters
*BIME for Bacterial Interspersed Mosaic Element
*genotoxic agents
*bacterial super-integrons
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
=External Links=
[http://www.pasteur.fr/recherche/unites/pmtg/about.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

ERIC

2006-07-10T19:57:24Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Nicole Perna and Fred Blattner''
|-
| width='30%' | What:
| ''Enteropathogen Resource Integration Center''
|-
| Where:
| SRA International and Genome Center of Wisconsin [http://www.ericbrc.org/portal/eric/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
ERIC is one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.
[http://www.ericbrc.org/portal/eric/ {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
Access genome-specific information from list of genomes.
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://www.ericbrc.org/portal/eric/ {{PAGENAME}}]
 ASAP
==Discussion of {{PAGENAME}} on other websites==

ERIC

2006-07-10T19:55:35Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Nicole Perna and Fred Blattner''
|-
| width='30%' | What:
| ''Enteropathogen Resource Integration Center''
|-
| Where:
| SRA International and Genome Center of Wisconsin [http://www.ericbrc.org/portal/eric/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
ERIC is one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.
[http://www.ericbrc.org/portal/eric/ {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
Access genome-specific information from list of genomes.
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://www.ericbrc.org/portal/eric/ {{PAGENAME}}]
ASAP
==Discussion of {{PAGENAME}} on other websites==

ERIC

2006-07-10T19:47:59Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ERIC {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://ERIC {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ERIC {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

BSGI

2006-07-10T19:40:46Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Miroslaw Cygler''
|-
| width='30%' | What:
| ''BSGI: Bacterial Structural Genomics Initiative''
|-
| Where:
| NRC Biotechnology Research Institute [http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Protein structure for E. coli and Salmonella.
[http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
Browse list of target proteins and status for 3D structure determination. Where available, links to PDB are provided.
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
Raymond S, O'Toole N, Cygler, M. A data management system for structural genomics.
Proteome Sci. 2004 Jun 21;2(1):4.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=15210054&query_hl=7&itool=pubmed_docsum
=External Links=
[http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

BSGI

2006-07-10T19:36:21Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''BSGI: Bacterial Structural Genomics Initiative''
|-
| Where:
| [http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Protein structure for E. coli and Salmonella.
[http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
Browse list of target proteins and status for 3D structure determination. Where available, links to PDB are provided.
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
O'Toole N, Grabowski M, Otwinowski Z, Minor W, Cygler M. The structural genomics experimental pipeline: Insights from global target lists. Proteins. 2004 Aug 1;56(2):201-10.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=15211505&query_hl=7&itool=pubmed_docsum
=External Links=
[http://sgen.bri.nrc.ca/brimsg/bsgi.html {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

BSGI

2006-07-10T19:29:09Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://BSGI {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://BSGI {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://BSGI {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T19:24:08Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Tim Gardner http://gardnerlab.bu.edu/''
|-
| width='30%' | What:
| ''E. coli Affymetrix data''
|-
| Where:
| Boston University [http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.

[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
Experiments: 189
Arrays: 445

=Using {{PAGENAME}}=
==Browsing==
==Searching==
Users can query M3D by choosing a project and a list of genes.
Data can be normalized (scaling by gene) prior to analysis.

http://m3d.bu.edu/cgi-bin/web/array/index.pl?db=E_coli_v3_Build_1

Presentation formats include:
*Heat Plot (genes vs experiments)
*Histogram of individual gene expression (one plot per gene)
*Histogram of all gene expression (one plot for N genes)
*Plot Expression of many genes as a function of one gene
*Link to download expression data

Average Array Replicates by:
*RMA
*GCRMA
*DchipPM
*DchipMM
*MAS5

Heat Plot Parameters:
*rescale data to within stddev of mean
*Order Genes By Correlation
*Order Experiments By Correlation

Heat Map coloring:
*Red/Blue
*Red/Green

M3D provides a meatalink to execute queries on N-browse, which is described as an interactive graphical browser for molecular interaction networks

http://nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false

==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
The following free software and libraries were used for array normalization and to develop M3D: dChip, Bioconductor (for GCRMA and RMA), gd, cgic, Cluster 3.0, and MySQL.
==Web Services/API==

=Discussion=

=References=
=External Links=
[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

E. coli Entry Point

2006-07-10T19:22:28Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Sydney Kustu''
|-
| width='30%' | What:
| ''E. coli functional annotation''
|-
| Where:
| University of California, Berkeley
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
'Kustu lab interface to functional annotation. Connection to microarray data is behind the scenes and password protected.
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

E. coli Entry Point

2006-07-10T19:21:21Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Sydney Kustu''
|-
| width='30%' | What:
| ''E. coli functional annotation''
|-
| Where:
| University of California, Berkeley
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
'Kustu lab interface to functional annotation. Connection to microarray data is behind the scenes and password protected.
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://E. coli Entry Point {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

E. coli Entry Point

2006-07-10T19:20:18Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Sydney Kustu''
|-
| width='30%' | What:
| ''E. coli functional annotation''
|-
| Where:
| University of California, Berkeley [http://coli.berkeley.edu/ecoli/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Kustu lab interface to functional annotation. Connection to microarray data is behind the scenes and password protected.''
[http://coli.berkeley.edu/ecoli/ {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://E. coli Entry Point {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

E. coli Entry Point

2006-07-10T19:13:43Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Sydney Kustu''
|-
| width='30%' | What:
| ''E. coli functional annotation and microarray data''
|-
| Where:
University of California, Berkeley
| [http://coli.berkeley.edu/ecoli/ {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://E. coli Entry Point {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://E. coli Entry Point {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

E. coli Entry Point

2006-07-10T19:10:09Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://E. coli Entry Point {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://E. coli Entry Point {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://E. coli Entry Point {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T19:00:32Z

Tconway: /* Technology */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Tim Gardner http://gardnerlab.bu.edu/''
|-
| width='30%' | What:
| ''E. coli Affymetrix data''
|-
| Where:
| Boston University [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.

[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
Experiments: 189
Arrays: 445

=Using {{PAGENAME}}=
==Browsing==
==Searching==
Users can query M3D by choosing a project and a list of genes.
Data can be normalized (scaling by gene) prior to analysis.

http://m3d.bu.edu/cgi-bin/web/array/index.pl?db=E_coli_v3_Build_1

Presentation formats include:
*Heat Plot (genes vs experiments)
*Histogram of individual gene expression (one plot per gene)
*Histogram of all gene expression (one plot for N genes)
*Plot Expression of many genes as a function of one gene
*Link to download expression data

Average Array Replicates by:
*RMA
*GCRMA
*DchipPM
*DchipMM
*MAS5

Heat Plot Parameters:
*rescale data to within stddev of mean
*Order Genes By Correlation
*Order Experiments By Correlation

Heat Map coloring:
*Red/Blue
*Red/Green

M3D provides a meatalink to execute queries on N-browse, which is described as an interactive graphical browser for molecular interaction networks

http://nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false

==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
The following free software and libraries were used for array normalization and to develop M3D: dChip, Bioconductor (for GCRMA and RMA), gd, cgic, Cluster 3.0, and MySQL.
==Web Services/API==

=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T18:58:46Z

Tconway: /* Searching */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Tim Gardner http://gardnerlab.bu.edu/''
|-
| width='30%' | What:
| ''E. coli Affymetrix data''
|-
| Where:
| Boston University [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.

[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
Experiments: 189
Arrays: 445

=Using {{PAGENAME}}=
==Browsing==
==Searching==
Users can query M3D by choosing a project and a list of genes.
Data can be normalized (scaling by gene) prior to analysis.

http://m3d.bu.edu/cgi-bin/web/array/index.pl?db=E_coli_v3_Build_1

Presentation formats include:
*Heat Plot (genes vs experiments)
*Histogram of individual gene expression (one plot per gene)
*Histogram of all gene expression (one plot for N genes)
*Plot Expression of many genes as a function of one gene
*Link to download expression data

Average Array Replicates by:
*RMA
*GCRMA
*DchipPM
*DchipMM
*MAS5

Heat Plot Parameters:
*rescale data to within stddev of mean
*Order Genes By Correlation
*Order Experiments By Correlation

Heat Map coloring:
*Red/Blue
*Red/Green

M3D provides a meatalink to execute queries on N-browse, which is described as an interactive graphical browser for molecular interaction networks

http://nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false

==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T18:45:09Z

Tconway: /* Content */

Many Microbe Microarrays Database (M3D)

2006-07-10T18:44:10Z

Tconway:

Many Microbe Microarrays Database (M3D)

2006-07-10T18:43:42Z

Tconway:

Many Microbe Microarrays Database (M3D)

2006-07-10T18:42:36Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''Tim Gardner, Boston University http://gardnerlab.bu.edu/''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.

[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T18:41:14Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.

[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T18:40:28Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Many Microbe Microarrays Database (M3D)

2006-07-10T18:39:17Z

Tconway:

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://ASAP {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://ASAP {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:54:01Z

Tconway: /* References */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
What is MiST?

The Microbial Signal Transduction database contains the signal transduction proteins for 354 complete bacterial and archaeal organisms. These are identified using various domain profiles that directly or indirectly implicate a particular protein in participating in signal transduction.

Browsing or searching by organism takes user to organismal overview of signal transduction systems, presumably deduced from genome sequence. Clicking on "2-component proteins" or "1-component proteins" takes user to list of regulators which provides additional information and domain architecture.

[http://genomics.ornl.gov/mist {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
Ulrich, L.E., Koonin, E.V., and Zhulin, I.B.
One-component systems dominate signal transduction in prokaryotes.
Trends in Microbiology, 13(2):52-6, Feb 2005.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15680762&query_hl=7&itool=pubmed_docsum

=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:52:43Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
What is MiST?

The Microbial Signal Transduction database contains the signal transduction proteins for 354 complete bacterial and archaeal organisms. These are identified using various domain profiles that directly or indirectly implicate a particular protein in participating in signal transduction.

Browsing or searching by organism takes user to organismal overview of signal transduction systems, presumably deduced from genome sequence. Clicking on "2-component proteins" or "1-component proteins" takes user to list of regulators which provides additional information and domain architecture.

[http://genomics.ornl.gov/mist {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:52:19Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
What is MiST?

The Microbial Signal Transduction database contains the signal transduction proteins for 354 complete bacterial and archaeal organisms. These are identified using various domain profiles that directly or indirectly implicate a particular protein in participating in signal transduction.

 Browsing or searching by organism takes user to organismal overview of signal transduction systems, presumably deduced from genome sequence. Clicking on "2-component proteins" or "1-component proteins" takes user to list of regulators which provides additional information and domain architecture.

[http://genomics.ornl.gov/mist {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:51:44Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
What is MiST?

The Microbial Signal Transduction database contains the signal transduction proteins for 354 complete bacterial and archaeal organisms. These are identified using various domain profiles that directly or indirectly implicate a particular protein in participating in signal transduction.
 Browsing or searching by organism takes user to organismal overview of signal transduction systems, presumably deduced from genome sequence. Clicking on "2-component proteins" or "1-component proteins" takes user to list of regulators which provides additional information and domain architecture.
[http://genomics.ornl.gov/mist {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:50:44Z

Tconway: /* About {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
Browsing or searching by organism takes user to organismla overview of signal transduction systems, presumably deduced from genome sequence. Clicking on "2-component proteins" or "1-component proteins" takes user to list of regulators which provides additional information and domain architecture.
[http://genomics.ornl.gov/mist {{PAGENAME}}] is...

=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

Microbial Signal Transduction (MiST)

2006-07-10T17:43:33Z

Tconway: /* Using {{PAGENAME}} */

{{Pagetop}}
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| Igor Zhulin, Oak Ridge National Laboratory
|-
| width='30%' | What:
| Signal transduction proteins from bacteria and archaea
|-
| Where:
| [http://genomics.ornl.gov/mist {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://genomics.ornl.gov/mist {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
*Browse by taxonomy http://genomics.ornl.gov/mist/select_organism.php
*Browse by organism list: http://genomics.ornl.gov/mist/organism_list.php
==Searching==
*Search by organism name in query box http://genomics.ornl.gov/mist/
*Search by GI number
==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=

=References=
=External Links=
[http://genomics.ornl.gov/mist {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

EcoCyc

2006-07-10T17:21:31Z

Tconway: /* Searching */

{{Pagetop}}
[[Category:Databases]][[Category:EcoliHub Partner]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| [[Peter Karp]], SRI
|-
| width='30%' | What:
| Comprehensive database of ''E. coli' molecular components
|-
| Where:
| [http://ecocyc.org {{PAGENAME}}]
|-
| Updates
| Every 3 months
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
[http://ecocyc.org {{PAGENAME}}] is a database of literature-based "gold standard" annotation of the molecular components of ''E. coli'' K-12, primarily referencing strain MG1655. EcoCyc is a central part of the [http://biocyc.org/ BioCyc] collection of database at [[wikipedia:SRI International|SRI International]] in Menlo Park, CA.

=Content=

Genes, Proteins, Compounds, and everything related.
All possible types of pathways

Reactions:
Binding
DNA repair
EC
Protein-Ligand
Reactions of Two Component Regulators
Transport Reactions
Unclassified Reaction

Any possible type of Compound

Metabolic chart
you can actually paint omics data onto the diagram

Omics Viewer

=Using {{PAGENAME}}=
==Browsing==
==Searching==
*"ENZYME">Protein (by name or EC#)
*" PATHWAY">Pathway (by name)
*" REACTION">Reaction (by name or EC#)
*" COMPOUND">Compound (by name)
*" GENE">Gene (by name)
*" RNA">RNA (by name) 
When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also specifically referenced, with the bibliography at the bottom of the linked page.
 query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

To get you started, here are a few things people generally want.

To get a sequence to enter into your Cloning software:

If you need the gene (start to stop codons) or protein sequence, click on the appropriate tab at the very top of the page. There is also a page that allows you to specify what range of DNA you want. To get back to the parC page, click the Back button of your browser. Very simple.

To see what genes flank your gene of interest:

Click on the genome browser link at the map position heading (4th heading down the page). You may see what flanks your gene as well as directionality. This tool resembles Google MapsTM, in that it has arrows that allow you to move along the gene map in either direction. To get back to the previous page, just click the Back button of your browser.

To see where the gene is w.r.t. other organisms:

Click on the "Align in Multiple-Genome Browser" tab. Next select the organisms you want to compare (the alphabetical list goes across), select "submit" and there it is. If at any time you want to change or add organisms to the alignment process, click on the "select allowed organisms" tab at the top of the page, and you are free to change your preferences.
You may also change the gene you are looking at from this page as well- up at the top.

==Usage examples==
''Add links to additional pages describing success stories here.''

These are other papers that cite the first paper listed in the reference section below. You could look at these for other examples of how this database is used.

'''The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons''' 
Víctor González, Rosa I. Santamaría, Patricia Bustos, Ismael Hernández-González, Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Sarath Chandra Janga, Miguel A. Ramírez, Verónica Jiménez-Jacinto, Julio Collado-Vides, and Guillermo Dávila
Proc Natl Acad Sci U S A. 2006 March 7; 103(10): 3834–3839. Published online 2006 February 27. doi: 10.1073/pnas.0508502103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1383491 Full text in PNAS]]

'''Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach'''
Swaine L. Chen, Chia-Seui Hung, Jian Xu, Christopher S. Reigstad, Vincent Magrini, Aniko Sabo, Darin Blasiar, Tamberlyn Bieri, Rekha R. Meyer, Philip Ozersky, Jon R. Armstrong, Robert S. Fulton, J. Phillip Latreille, John Spieth, Thomas M. Hooton, Elaine R. Mardis, Scott J. Hultgren, and Jeffrey I. Gordon
Proc Natl Acad Sci U S A. 2006 April 11; 103(15): 5977–5982. Published online 2006 April 3. doi: 10.1073/pnas.0600938103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1424661 Full text in PNAS]]

'''Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters'''
Dongying Wu, Sean C Daugherty, Susan E Van Aken, Grace H Pai, Kisha L Watkins, Hoda Khouri, Luke J Tallon, Jennifer M Zaborsky, Helen E Dunbar, Phat L Tran, Nancy A Moran, and Jonathan A Eisen
PLoS Biol. 2006 June; 4(6): e188. Published online 2006 June 6. doi: 10.1371/journal.pbio.0040188. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1472245 Full text in PLoS]]

'''Escherichia coli K-12: a cooperatively developed annotation snapshot—2005'''
Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner
Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 January 5. doi: 10.1093/nar/gkj405.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1325200 Full text in NAR]]

'''NPInter: the noncoding RNAs and protein related biomacromolecules interaction database'''
Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen
Nucleic Acids Res. 2006 January 1; 34(Database issue): D150–D152. Published online 2005 December 28. doi: 10.1093/nar/gkj025.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347388 Full text in NAR]]

'''MODOMICS: a database of RNA modification pathways'''
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki
Nucleic Acids Res. 2006 January 1; 34(Database issue): D145–D149. Published online 2005 December 28. doi: 10.1093/nar/gkj084.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347447 Full text in NAR]]

'''PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways'''
Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza
Nucleic Acids Res. 2006 January 1; 34(Database issue): D369–D372. Published online 2005 December 28. doi: 10.1093/nar/gkj095. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347457 Full text in NAR]]

'''MetaCyc: a multiorganism database of metabolic pathways and enzymes'''
Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp
Nucleic Acids Res. 2006 January 1; 34(Database issue): D511–D516. Published online 2005 December 28. doi: 10.1093/nar/gkj128. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347490 Full text in NAR]]

'''The UCSC Archaeal Genome Browser'''
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe
Nucleic Acids Res. 2006 January 1; 34(Database issue): D407–D410. Published online 2005 December 28. doi: 10.1093/nar/gkj134. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347496 Full text in NAR]]

'''RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions'''
Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides
Nucleic Acids Res. 2006 January 1; 34(Database issue): D394–D397. Published online 2005 December 28. doi: 10.1093/nar/gkj156. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347518 Full text in NAR]]

'''The comprehensive updated regulatory network of Escherichia coli K-12'''
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, and Julio Collado-Vides
BMC Bioinformatics. 2006; 7: 5. Published online 2006 January 6. doi: 10.1186/1471-2105-7-5. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1382256 Full text in BMC Bioinformatics]]

'''Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms'''
Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, and Roland Eils
BMC Bioinformatics. 2006; 7: 119. Published online 2006 March 8. doi: 10.1186/1471-2105-7-119. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1434775 Full text in BMC Bioinformatics]]

'''GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes'''
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, and Masaru Tomita
BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1435936 Full text in BMC Bioinformatics]]

'''Detecting uber-operons in prokaryotic genomes'''
Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu
Nucleic Acids Res. 2006; 34(8): 2418–2427. Published online 2006 May 8. doi: 10.1093/nar/gkl294. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1458513 Full text in NAR]]

'''Structure and function of negative feedback loops at the interface of genetic and metabolic networks'''
Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen
Nucleic Acids Res. 2006; 34(8): 2455–2462. Published online 2006 May 9. doi: 10.1093/nar/gkl140. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1459064 Full text in NAR]]

'''In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments'''
Bas Teusink, Frank H. J. van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J. Smid, and Roland J. Siezen
Appl Environ Microbiol. 2005 November; 71(11): 7253–7262. doi: 10.1128/AEM.71.11.7253-7262.2005. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1287688 Full text in AEM]]

'''Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states'''
Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson
Genome Res. 2005 October; 15(10): 1365–1372. doi: 10.1101/gr.3832305. [[http://www.genome.org/cgi/content/full/15/10/1365 Full text in Genome Research]]

'''MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research'''
Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee
Plant Physiol. 2005 May; 138(1): 27–37. doi: 10.1104/pp.105.060376. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1104157 Full text in Plant Phys]]

'''Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers'''
M. L. Green and P. D. Karp
Nucleic Acids Res. 2005; 33(13): 4035–4039. Published online 2005 July 20. doi: 10.1093/nar/gki711. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1179732 Full text in NAR]]

'''sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes'''
Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor
Nucleic Acids Res. 2005; 33(13): 4096–4105. Published online 2005 July 26. doi: 10.1093/nar/gki715. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1180744 Full text in NAR]]

'''Expansion of the BioCyc collection of pathway/genome databases to 160 genomes'''
Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas
Nucleic Acids Res. 2005; 33(19): 6083–6089. Published online 2005 October 24. doi: 10.1093/nar/gki892. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1266070 Full text in NAR]]

=Other sites with related content=
=Technology=
EcoCyc is written in LISP. It runs in two modes: the desktop mode has more extenisve features and the webserver mode provides information via the Internet. 
More information on EcoCyc programming is available: [http://biocyc.org/desktop-vs-web-mode.shtml EcoCyc Modes]
==Web Services/API==

=Discussion=

=References=

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp.
'''EcoCyc: A comprehensive database resource for Escherichia coli''',
Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L.,
'''Escherichia coli K-12: a cooperatively developed annotation snapshot--2005'''
Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J.,
'''The comprehensive updated regulatory network of Escherichia coli K-12'''
BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr.,
'''The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database'''
ASM News 70(1):25-30 2004.

=External Links=
[http://ecocyc.org {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

EcoCyc

2006-07-10T17:15:53Z

Tconway: /* Technology */

{{Pagetop}}
[[Category:Databases]][[Category:EcoliHub Partner]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| [[Peter Karp]], SRI
|-
| width='30%' | What:
| Comprehensive database of ''E. coli' molecular components
|-
| Where:
| [http://ecocyc.org {{PAGENAME}}]
|-
| Updates
| Every 3 months
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
[http://ecocyc.org {{PAGENAME}}] is a database of literature-based "gold standard" annotation of the molecular components of ''E. coli'' K-12, primarily referencing strain MG1655. EcoCyc is a central part of the [http://biocyc.org/ BioCyc] collection of database at [[wikipedia:SRI International|SRI International]] in Menlo Park, CA.

=Content=

Genes, Proteins, Compounds, and everything related.
All possible types of pathways

Reactions:
Binding
DNA repair
EC
Protein-Ligand
Reactions of Two Component Regulators
Transport Reactions
Unclassified Reaction

Any possible type of Compound

Metabolic chart
you can actually paint omics data onto the diagram

Omics Viewer

=Using {{PAGENAME}}=
==Browsing==
==Searching==

When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also specifically referenced, with the bibliography at the bottom of the linked page.
 query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

To get you started, here are a few things people generally want.

To get a sequence to enter into your Cloning software:

If you need the gene (start to stop codons) or protein sequence, click on the appropriate tab at the very top of the page. There is also a page that allows you to specify what range of DNA you want. To get back to the parC page, click the Back button of your browser. Very simple.

To see what genes flank your gene of interest:

Click on the genome browser link at the map position heading (4th heading down the page). You may see what flanks your gene as well as directionality. This tool resembles Google MapsTM, in that it has arrows that allow you to move along the gene map in either direction. To get back to the previous page, just click the Back button of your browser.

To see where the gene is w.r.t. other organisms:

Click on the "Align in Multiple-Genome Browser" tab. Next select the organisms you want to compare (the alphabetical list goes across), select "submit" and there it is. If at any time you want to change or add organisms to the alignment process, click on the "select allowed organisms" tab at the top of the page, and you are free to change your preferences.
You may also change the gene you are looking at from this page as well- up at the top.

==Usage examples==
''Add links to additional pages describing success stories here.''

These are other papers that cite the first paper listed in the reference section below. You could look at these for other examples of how this database is used.

'''The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons''' 
Víctor González, Rosa I. Santamaría, Patricia Bustos, Ismael Hernández-González, Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Sarath Chandra Janga, Miguel A. Ramírez, Verónica Jiménez-Jacinto, Julio Collado-Vides, and Guillermo Dávila
Proc Natl Acad Sci U S A. 2006 March 7; 103(10): 3834–3839. Published online 2006 February 27. doi: 10.1073/pnas.0508502103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1383491 Full text in PNAS]]

'''Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach'''
Swaine L. Chen, Chia-Seui Hung, Jian Xu, Christopher S. Reigstad, Vincent Magrini, Aniko Sabo, Darin Blasiar, Tamberlyn Bieri, Rekha R. Meyer, Philip Ozersky, Jon R. Armstrong, Robert S. Fulton, J. Phillip Latreille, John Spieth, Thomas M. Hooton, Elaine R. Mardis, Scott J. Hultgren, and Jeffrey I. Gordon
Proc Natl Acad Sci U S A. 2006 April 11; 103(15): 5977–5982. Published online 2006 April 3. doi: 10.1073/pnas.0600938103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1424661 Full text in PNAS]]

'''Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters'''
Dongying Wu, Sean C Daugherty, Susan E Van Aken, Grace H Pai, Kisha L Watkins, Hoda Khouri, Luke J Tallon, Jennifer M Zaborsky, Helen E Dunbar, Phat L Tran, Nancy A Moran, and Jonathan A Eisen
PLoS Biol. 2006 June; 4(6): e188. Published online 2006 June 6. doi: 10.1371/journal.pbio.0040188. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1472245 Full text in PLoS]]

'''Escherichia coli K-12: a cooperatively developed annotation snapshot—2005'''
Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner
Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 January 5. doi: 10.1093/nar/gkj405.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1325200 Full text in NAR]]

'''NPInter: the noncoding RNAs and protein related biomacromolecules interaction database'''
Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen
Nucleic Acids Res. 2006 January 1; 34(Database issue): D150–D152. Published online 2005 December 28. doi: 10.1093/nar/gkj025.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347388 Full text in NAR]]

'''MODOMICS: a database of RNA modification pathways'''
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki
Nucleic Acids Res. 2006 January 1; 34(Database issue): D145–D149. Published online 2005 December 28. doi: 10.1093/nar/gkj084.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347447 Full text in NAR]]

'''PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways'''
Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza
Nucleic Acids Res. 2006 January 1; 34(Database issue): D369–D372. Published online 2005 December 28. doi: 10.1093/nar/gkj095. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347457 Full text in NAR]]

'''MetaCyc: a multiorganism database of metabolic pathways and enzymes'''
Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp
Nucleic Acids Res. 2006 January 1; 34(Database issue): D511–D516. Published online 2005 December 28. doi: 10.1093/nar/gkj128. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347490 Full text in NAR]]

'''The UCSC Archaeal Genome Browser'''
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe
Nucleic Acids Res. 2006 January 1; 34(Database issue): D407–D410. Published online 2005 December 28. doi: 10.1093/nar/gkj134. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347496 Full text in NAR]]

'''RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions'''
Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides
Nucleic Acids Res. 2006 January 1; 34(Database issue): D394–D397. Published online 2005 December 28. doi: 10.1093/nar/gkj156. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347518 Full text in NAR]]

'''The comprehensive updated regulatory network of Escherichia coli K-12'''
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, and Julio Collado-Vides
BMC Bioinformatics. 2006; 7: 5. Published online 2006 January 6. doi: 10.1186/1471-2105-7-5. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1382256 Full text in BMC Bioinformatics]]

'''Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms'''
Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, and Roland Eils
BMC Bioinformatics. 2006; 7: 119. Published online 2006 March 8. doi: 10.1186/1471-2105-7-119. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1434775 Full text in BMC Bioinformatics]]

'''GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes'''
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, and Masaru Tomita
BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1435936 Full text in BMC Bioinformatics]]

'''Detecting uber-operons in prokaryotic genomes'''
Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu
Nucleic Acids Res. 2006; 34(8): 2418–2427. Published online 2006 May 8. doi: 10.1093/nar/gkl294. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1458513 Full text in NAR]]

'''Structure and function of negative feedback loops at the interface of genetic and metabolic networks'''
Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen
Nucleic Acids Res. 2006; 34(8): 2455–2462. Published online 2006 May 9. doi: 10.1093/nar/gkl140. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1459064 Full text in NAR]]

'''In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments'''
Bas Teusink, Frank H. J. van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J. Smid, and Roland J. Siezen
Appl Environ Microbiol. 2005 November; 71(11): 7253–7262. doi: 10.1128/AEM.71.11.7253-7262.2005. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1287688 Full text in AEM]]

'''Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states'''
Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson
Genome Res. 2005 October; 15(10): 1365–1372. doi: 10.1101/gr.3832305. [[http://www.genome.org/cgi/content/full/15/10/1365 Full text in Genome Research]]

'''MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research'''
Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee
Plant Physiol. 2005 May; 138(1): 27–37. doi: 10.1104/pp.105.060376. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1104157 Full text in Plant Phys]]

'''Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers'''
M. L. Green and P. D. Karp
Nucleic Acids Res. 2005; 33(13): 4035–4039. Published online 2005 July 20. doi: 10.1093/nar/gki711. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1179732 Full text in NAR]]

'''sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes'''
Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor
Nucleic Acids Res. 2005; 33(13): 4096–4105. Published online 2005 July 26. doi: 10.1093/nar/gki715. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1180744 Full text in NAR]]

'''Expansion of the BioCyc collection of pathway/genome databases to 160 genomes'''
Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas
Nucleic Acids Res. 2005; 33(19): 6083–6089. Published online 2005 October 24. doi: 10.1093/nar/gki892. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1266070 Full text in NAR]]

=Other sites with related content=
=Technology=
EcoCyc is written in LISP. It runs in two modes: the desktop mode has more extenisve features and the webserver mode provides information via the Internet. 
More information on EcoCyc programming is available: [http://biocyc.org/desktop-vs-web-mode.shtml EcoCyc Modes]
==Web Services/API==

=Discussion=

=References=

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp.
'''EcoCyc: A comprehensive database resource for Escherichia coli''',
Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L.,
'''Escherichia coli K-12: a cooperatively developed annotation snapshot--2005'''
Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J.,
'''The comprehensive updated regulatory network of Escherichia coli K-12'''
BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr.,
'''The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database'''
ASM News 70(1):25-30 2004.

=External Links=
[http://ecocyc.org {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

EcoCyc

2006-07-10T17:12:58Z

Tconway: /* Technology */

{{Pagetop}}
[[Category:Databases]][[Category:EcoliHub Partner]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| [[Peter Karp]], SRI
|-
| width='30%' | What:
| Comprehensive database of ''E. coli' molecular components
|-
| Where:
| [http://ecocyc.org {{PAGENAME}}]
|-
| Updates
| Every 3 months
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
[http://ecocyc.org {{PAGENAME}}] is a database of literature-based "gold standard" annotation of the molecular components of ''E. coli'' K-12, primarily referencing strain MG1655. EcoCyc is a central part of the [http://biocyc.org/ BioCyc] collection of database at [[wikipedia:SRI International|SRI International]] in Menlo Park, CA.

=Content=

Genes, Proteins, Compounds, and everything related.
All possible types of pathways

Reactions:
Binding
DNA repair
EC
Protein-Ligand
Reactions of Two Component Regulators
Transport Reactions
Unclassified Reaction

Any possible type of Compound

Metabolic chart
you can actually paint omics data onto the diagram

Omics Viewer

=Using {{PAGENAME}}=
==Browsing==
==Searching==

When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also specifically referenced, with the bibliography at the bottom of the linked page.
 query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

To get you started, here are a few things people generally want.

To get a sequence to enter into your Cloning software:

If you need the gene (start to stop codons) or protein sequence, click on the appropriate tab at the very top of the page. There is also a page that allows you to specify what range of DNA you want. To get back to the parC page, click the Back button of your browser. Very simple.

To see what genes flank your gene of interest:

Click on the genome browser link at the map position heading (4th heading down the page). You may see what flanks your gene as well as directionality. This tool resembles Google MapsTM, in that it has arrows that allow you to move along the gene map in either direction. To get back to the previous page, just click the Back button of your browser.

To see where the gene is w.r.t. other organisms:

Click on the "Align in Multiple-Genome Browser" tab. Next select the organisms you want to compare (the alphabetical list goes across), select "submit" and there it is. If at any time you want to change or add organisms to the alignment process, click on the "select allowed organisms" tab at the top of the page, and you are free to change your preferences.
You may also change the gene you are looking at from this page as well- up at the top.

==Usage examples==
''Add links to additional pages describing success stories here.''

These are other papers that cite the first paper listed in the reference section below. You could look at these for other examples of how this database is used.

'''The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons''' 
Víctor González, Rosa I. Santamaría, Patricia Bustos, Ismael Hernández-González, Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Sarath Chandra Janga, Miguel A. Ramírez, Verónica Jiménez-Jacinto, Julio Collado-Vides, and Guillermo Dávila
Proc Natl Acad Sci U S A. 2006 March 7; 103(10): 3834–3839. Published online 2006 February 27. doi: 10.1073/pnas.0508502103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1383491 Full text in PNAS]]

'''Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach'''
Swaine L. Chen, Chia-Seui Hung, Jian Xu, Christopher S. Reigstad, Vincent Magrini, Aniko Sabo, Darin Blasiar, Tamberlyn Bieri, Rekha R. Meyer, Philip Ozersky, Jon R. Armstrong, Robert S. Fulton, J. Phillip Latreille, John Spieth, Thomas M. Hooton, Elaine R. Mardis, Scott J. Hultgren, and Jeffrey I. Gordon
Proc Natl Acad Sci U S A. 2006 April 11; 103(15): 5977–5982. Published online 2006 April 3. doi: 10.1073/pnas.0600938103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1424661 Full text in PNAS]]

'''Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters'''
Dongying Wu, Sean C Daugherty, Susan E Van Aken, Grace H Pai, Kisha L Watkins, Hoda Khouri, Luke J Tallon, Jennifer M Zaborsky, Helen E Dunbar, Phat L Tran, Nancy A Moran, and Jonathan A Eisen
PLoS Biol. 2006 June; 4(6): e188. Published online 2006 June 6. doi: 10.1371/journal.pbio.0040188. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1472245 Full text in PLoS]]

'''Escherichia coli K-12: a cooperatively developed annotation snapshot—2005'''
Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner
Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 January 5. doi: 10.1093/nar/gkj405.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1325200 Full text in NAR]]

'''NPInter: the noncoding RNAs and protein related biomacromolecules interaction database'''
Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen
Nucleic Acids Res. 2006 January 1; 34(Database issue): D150–D152. Published online 2005 December 28. doi: 10.1093/nar/gkj025.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347388 Full text in NAR]]

'''MODOMICS: a database of RNA modification pathways'''
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki
Nucleic Acids Res. 2006 January 1; 34(Database issue): D145–D149. Published online 2005 December 28. doi: 10.1093/nar/gkj084.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347447 Full text in NAR]]

'''PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways'''
Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza
Nucleic Acids Res. 2006 January 1; 34(Database issue): D369–D372. Published online 2005 December 28. doi: 10.1093/nar/gkj095. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347457 Full text in NAR]]

'''MetaCyc: a multiorganism database of metabolic pathways and enzymes'''
Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp
Nucleic Acids Res. 2006 January 1; 34(Database issue): D511–D516. Published online 2005 December 28. doi: 10.1093/nar/gkj128. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347490 Full text in NAR]]

'''The UCSC Archaeal Genome Browser'''
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe
Nucleic Acids Res. 2006 January 1; 34(Database issue): D407–D410. Published online 2005 December 28. doi: 10.1093/nar/gkj134. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347496 Full text in NAR]]

'''RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions'''
Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides
Nucleic Acids Res. 2006 January 1; 34(Database issue): D394–D397. Published online 2005 December 28. doi: 10.1093/nar/gkj156. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347518 Full text in NAR]]

'''The comprehensive updated regulatory network of Escherichia coli K-12'''
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, and Julio Collado-Vides
BMC Bioinformatics. 2006; 7: 5. Published online 2006 January 6. doi: 10.1186/1471-2105-7-5. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1382256 Full text in BMC Bioinformatics]]

'''Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms'''
Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, and Roland Eils
BMC Bioinformatics. 2006; 7: 119. Published online 2006 March 8. doi: 10.1186/1471-2105-7-119. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1434775 Full text in BMC Bioinformatics]]

'''GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes'''
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, and Masaru Tomita
BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1435936 Full text in BMC Bioinformatics]]

'''Detecting uber-operons in prokaryotic genomes'''
Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu
Nucleic Acids Res. 2006; 34(8): 2418–2427. Published online 2006 May 8. doi: 10.1093/nar/gkl294. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1458513 Full text in NAR]]

'''Structure and function of negative feedback loops at the interface of genetic and metabolic networks'''
Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen
Nucleic Acids Res. 2006; 34(8): 2455–2462. Published online 2006 May 9. doi: 10.1093/nar/gkl140. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1459064 Full text in NAR]]

'''In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments'''
Bas Teusink, Frank H. J. van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J. Smid, and Roland J. Siezen
Appl Environ Microbiol. 2005 November; 71(11): 7253–7262. doi: 10.1128/AEM.71.11.7253-7262.2005. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1287688 Full text in AEM]]

'''Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states'''
Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson
Genome Res. 2005 October; 15(10): 1365–1372. doi: 10.1101/gr.3832305. [[http://www.genome.org/cgi/content/full/15/10/1365 Full text in Genome Research]]

'''MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research'''
Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee
Plant Physiol. 2005 May; 138(1): 27–37. doi: 10.1104/pp.105.060376. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1104157 Full text in Plant Phys]]

'''Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers'''
M. L. Green and P. D. Karp
Nucleic Acids Res. 2005; 33(13): 4035–4039. Published online 2005 July 20. doi: 10.1093/nar/gki711. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1179732 Full text in NAR]]

'''sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes'''
Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor
Nucleic Acids Res. 2005; 33(13): 4096–4105. Published online 2005 July 26. doi: 10.1093/nar/gki715. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1180744 Full text in NAR]]

'''Expansion of the BioCyc collection of pathway/genome databases to 160 genomes'''
Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas
Nucleic Acids Res. 2005; 33(19): 6083–6089. Published online 2005 October 24. doi: 10.1093/nar/gki892. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1266070 Full text in NAR]]

=Other sites with related content=
=Technology=
EcoCyc is written in LISP. It runs in two modes: the desktop mode has more extenisve features and the webserver mode provides information via the Internet. 
More information on EcoCyc programming is available: [http://biocyc.org/desktop-vs-web-mode.shtml]
==Web Services/API==

=Discussion=

=References=

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp.
'''EcoCyc: A comprehensive database resource for Escherichia coli''',
Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L.,
'''Escherichia coli K-12: a cooperatively developed annotation snapshot--2005'''
Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J.,
'''The comprehensive updated regulatory network of Escherichia coli K-12'''
BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr.,
'''The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database'''
ASM News 70(1):25-30 2004.

=External Links=
[http://ecocyc.org {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

EcoCyc

2006-07-10T17:11:42Z

Tconway: /* Technology */

{{Pagetop}}
[[Category:Databases]][[Category:EcoliHub Partner]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| [[Peter Karp]], SRI
|-
| width='30%' | What:
| Comprehensive database of ''E. coli' molecular components
|-
| Where:
| [http://ecocyc.org {{PAGENAME}}]
|-
| Updates
| Every 3 months
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
[http://ecocyc.org {{PAGENAME}}] is a database of literature-based "gold standard" annotation of the molecular components of ''E. coli'' K-12, primarily referencing strain MG1655. EcoCyc is a central part of the [http://biocyc.org/ BioCyc] collection of database at [[wikipedia:SRI International|SRI International]] in Menlo Park, CA.

=Content=

Genes, Proteins, Compounds, and everything related.
All possible types of pathways

Reactions:
Binding
DNA repair
EC
Protein-Ligand
Reactions of Two Component Regulators
Transport Reactions
Unclassified Reaction

Any possible type of Compound

Metabolic chart
you can actually paint omics data onto the diagram

Omics Viewer

=Using {{PAGENAME}}=
==Browsing==
==Searching==

When the input is a gene or protein:

This db tells you practically everything you ever wanted to know about a gene or protein. When you insert the query, the output allows a decision between the gene or its protein product. Most of the information is in the form of links. In fact, 90% of the page is link-able, which could get messy if you don't quite know what you are looking for. The information in EcoCyc is also specifically referenced, with the bibliography at the bottom of the linked page.
 query by EG# (http://ecocyc.org/ECOLI/new-image?type=GENE&object=EG10257)

To get you started, here are a few things people generally want.

To get a sequence to enter into your Cloning software:

If you need the gene (start to stop codons) or protein sequence, click on the appropriate tab at the very top of the page. There is also a page that allows you to specify what range of DNA you want. To get back to the parC page, click the Back button of your browser. Very simple.

To see what genes flank your gene of interest:

Click on the genome browser link at the map position heading (4th heading down the page). You may see what flanks your gene as well as directionality. This tool resembles Google MapsTM, in that it has arrows that allow you to move along the gene map in either direction. To get back to the previous page, just click the Back button of your browser.

To see where the gene is w.r.t. other organisms:

Click on the "Align in Multiple-Genome Browser" tab. Next select the organisms you want to compare (the alphabetical list goes across), select "submit" and there it is. If at any time you want to change or add organisms to the alignment process, click on the "select allowed organisms" tab at the top of the page, and you are free to change your preferences.
You may also change the gene you are looking at from this page as well- up at the top.

==Usage examples==
''Add links to additional pages describing success stories here.''

These are other papers that cite the first paper listed in the reference section below. You could look at these for other examples of how this database is used.

'''The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons''' 
Víctor González, Rosa I. Santamaría, Patricia Bustos, Ismael Hernández-González, Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Sarath Chandra Janga, Miguel A. Ramírez, Verónica Jiménez-Jacinto, Julio Collado-Vides, and Guillermo Dávila
Proc Natl Acad Sci U S A. 2006 March 7; 103(10): 3834–3839. Published online 2006 February 27. doi: 10.1073/pnas.0508502103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1383491 Full text in PNAS]]

'''Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: A comparative genomics approach'''
Swaine L. Chen, Chia-Seui Hung, Jian Xu, Christopher S. Reigstad, Vincent Magrini, Aniko Sabo, Darin Blasiar, Tamberlyn Bieri, Rekha R. Meyer, Philip Ozersky, Jon R. Armstrong, Robert S. Fulton, J. Phillip Latreille, John Spieth, Thomas M. Hooton, Elaine R. Mardis, Scott J. Hultgren, and Jeffrey I. Gordon
Proc Natl Acad Sci U S A. 2006 April 11; 103(15): 5977–5982. Published online 2006 April 3. doi: 10.1073/pnas.0600938103. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1424661 Full text in PNAS]]

'''Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters'''
Dongying Wu, Sean C Daugherty, Susan E Van Aken, Grace H Pai, Kisha L Watkins, Hoda Khouri, Luke J Tallon, Jennifer M Zaborsky, Helen E Dunbar, Phat L Tran, Nancy A Moran, and Jonathan A Eisen
PLoS Biol. 2006 June; 4(6): e188. Published online 2006 June 6. doi: 10.1371/journal.pbio.0040188. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1472245 Full text in PLoS]]

'''Escherichia coli K-12: a cooperatively developed annotation snapshot—2005'''
Monica Riley, Takashi Abe, Martha B. Arnaud, Mary K.B. Berlyn, Frederick R. Blattner, Roy R. Chaudhuri, Jeremy D. Glasner, Takashi Horiuchi, Ingrid M. Keseler, Takehide Kosuge, Hirotada Mori, Nicole T. Perna, Guy Plunkett, III, Kenneth E. Rudd, Margrethe H. Serres, Gavin H. Thomas, Nicholas R. Thomson, David Wishart, and Barry L. Wanner
Nucleic Acids Res. 2006; 34(1): 1–9. Published online 2006 January 5. doi: 10.1093/nar/gkj405.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1325200 Full text in NAR]]

'''NPInter: the noncoding RNAs and protein related biomacromolecules interaction database'''
Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, and Runsheng Chen
Nucleic Acids Res. 2006 January 1; 34(Database issue): D150–D152. Published online 2005 December 28. doi: 10.1093/nar/gkj025.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347388 Full text in NAR]]

'''MODOMICS: a database of RNA modification pathways'''
Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, and Janusz M. Bujnicki
Nucleic Acids Res. 2006 January 1; 34(Database issue): D145–D149. Published online 2005 December 28. doi: 10.1093/nar/gkj084.[[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347447 Full text in NAR]]

'''PUMA2—grid-based high-throughput analysis of genomes and metabolic pathways'''
Natalia Maltsev, Elizabeth Glass, Dinanath Sulakhe, Alexis Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, and Mark D'Souza
Nucleic Acids Res. 2006 January 1; 34(Database issue): D369–D372. Published online 2005 December 28. doi: 10.1093/nar/gkj095. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347457 Full text in NAR]]

'''MetaCyc: a multiorganism database of metabolic pathways and enzymes'''
Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y. Rhee, Christophe Tissier, Peifen Zhang, and Peter D. Karp
Nucleic Acids Res. 2006 January 1; 34(Database issue): D511–D516. Published online 2005 December 28. doi: 10.1093/nar/gkj128. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347490 Full text in NAR]]

'''The UCSC Archaeal Genome Browser'''
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, and Todd M. Lowe
Nucleic Acids Res. 2006 January 1; 34(Database issue): D407–D410. Published online 2005 December 28. doi: 10.1093/nar/gkj134. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347496 Full text in NAR]]

'''RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions'''
Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, and Julio Collado-Vides
Nucleic Acids Res. 2006 January 1; 34(Database issue): D394–D397. Published online 2005 December 28. doi: 10.1093/nar/gkj156. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1347518 Full text in NAR]]

'''The comprehensive updated regulatory network of Escherichia coli K-12'''
Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Martín Peralta-Gil, Mónica I Peñaloza-Spínola, Agustino Martínez-Antonio, Peter D Karp, and Julio Collado-Vides
BMC Bioinformatics. 2006; 7: 5. Published online 2006 January 6. doi: 10.1186/1471-2105-7-5. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1382256 Full text in BMC Bioinformatics]]

'''Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms'''
Rainer König, Gunnar Schramm, Marcus Oswald, Hanna Seitz, Sebastian Sager, Marc Zapatka, Gerhard Reinelt, and Roland Eils
BMC Bioinformatics. 2006; 7: 119. Published online 2006 March 8. doi: 10.1186/1471-2105-7-119. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1434775 Full text in BMC Bioinformatics]]

'''GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes'''
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, and Masaru Tomita
BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1435936 Full text in BMC Bioinformatics]]

'''Detecting uber-operons in prokaryotic genomes'''
Dongsheng Che, Guojun Li, Fenglou Mao, Hongwei Wu, and Ying Xu
Nucleic Acids Res. 2006; 34(8): 2418–2427. Published online 2006 May 8. doi: 10.1093/nar/gkl294. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1458513 Full text in NAR]]

'''Structure and function of negative feedback loops at the interface of genetic and metabolic networks'''
Sandeep Krishna, Anna M. C. Andersson, Szabolcs Semsey, and Kim Sneppen
Nucleic Acids Res. 2006; 34(8): 2455–2462. Published online 2006 May 9. doi: 10.1093/nar/gkl140. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1459064 Full text in NAR]]

'''In Silico Reconstruction of the Metabolic Pathways of Lactobacillus plantarum: Comparing Predictions of Nutrient Requirements with Those from Growth Experiments'''
Bas Teusink, Frank H. J. van Enckevort, Christof Francke, Anne Wiersma, Arno Wegkamp, Eddy J. Smid, and Roland J. Siezen
Appl Environ Microbiol. 2005 November; 71(11): 7253–7262. doi: 10.1128/AEM.71.11.7253-7262.2005. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1287688 Full text in AEM]]

'''Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states'''
Stephen S. Fong, Andrew R. Joyce, and Bernhard Ø. Palsson
Genome Res. 2005 October; 15(10): 1365–1372. doi: 10.1101/gr.3832305. [[http://www.genome.org/cgi/content/full/15/10/1365 Full text in Genome Research]]

'''MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research'''
Peifen Zhang, Hartmut Foerster, Christophe P. Tissier, Lukas Mueller, Suzanne Paley, Peter D. Karp, and Seung Y. Rhee
Plant Physiol. 2005 May; 138(1): 27–37. doi: 10.1104/pp.105.060376. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1104157 Full text in Plant Phys]]

'''Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers'''
M. L. Green and P. D. Karp
Nucleic Acids Res. 2005; 33(13): 4035–4039. Published online 2005 July 20. doi: 10.1093/nar/gki711. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1179732 Full text in NAR]]

'''sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes'''
Jonathan Livny, Michael A. Fogel, Brigid M. Davis, and Matthew K. Waldor
Nucleic Acids Res. 2005; 33(13): 4096–4105. Published online 2005 July 26. doi: 10.1093/nar/gki715. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1180744 Full text in NAR]]

'''Expansion of the BioCyc collection of pathway/genome databases to 160 genomes'''
Peter D. Karp, Christos A. Ouzounis, Caroline Moore-Kochlacs, Leon Goldovsky, Pallavi Kaipa, Dag Ahrén, Sophia Tsoka, Nikos Darzentas, Victor Kunin, and Núria López-Bigas
Nucleic Acids Res. 2005; 33(19): 6083–6089. Published online 2005 October 24. doi: 10.1093/nar/gki892. [[http://www.pubmedcentral.gov/articlerender.fcgi?artid=1266070 Full text in NAR]]

=Other sites with related content=
=Technology=
EcoCyc is written in LISP. It runs in two modes: the desktop mode has more extenisve features and the webserver mode provides information via the Internet.
==Web Services/API==

=Discussion=

=References=

I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp.
'''EcoCyc: A comprehensive database resource for Escherichia coli''',
Nucleic Acids Research 33:D334-7 2005.

See Also

Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L.,
'''Escherichia coli K-12: a cooperatively developed annotation snapshot--2005'''
Nucleic Acids Research 34:1-9 2006.

Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J.,
'''The comprehensive updated regulatory network of Escherichia coli K-12'''
BMC Bioinformatics 7:5 2006.

Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., and Saier M.H. Jr.,
'''The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database'''
ASM News 70(1):25-30 2004.

=External Links=
[http://ecocyc.org {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==

ExPASy proteomics server

2006-06-27T19:32:35Z

Tconway: /* Searching */

'''ExPASy'''
'''You can help [[EcoliWiki]] by editing the content of this page. For information about obtaining editing privileges, see [[E._coli_Wiki:Membership]]'''
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
|- align='center' bgcolor = '#ddddff'
| colspan = '2' | '''{{PAGENAME}}'''
|-
| width='30%' | Who:
| ''proprietor''
|-
| width='30%' | What:
| ''short description''
|-
| Where:
| [http://www.expasy.org/ ExPASy {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=
''Add general information here''
[http://www.expasy.org/ ExPASy {{PAGENAME}}] is...
=Content=
=Using {{PAGENAME}}=
==Browsing==
==Searching==
query by Swiss-Prot# (http://ca.expasy.org/cgi-bin/get-entries?AC=P25530) 
EC# mapped to b# (http://us.expasy.org/cgi-bin/nicezyme.pl?4.2.1.12)

==Usage examples==
''Add links to additional pages describing success stories here.''

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
[[Trackbacks|''What are trackbacks?'']] ''This feature is not yet functional''

=References=
=External Links=
[http://www.expasy.org/ ExPASy {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==