EcoliWiki - User contributions [en]

EcoGene

2006-06-21T03:42:22Z

Jiang7: /* Searching */

'''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://ecogene.org {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

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

==Searching==
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

{| {{Prettytable}}
| width='25%' | '''Input'''
| width='40%' | '''Output'''
|-
| width='25%' |
*Gene Name (DNA, RNA, or pseudo gene)
*Synonym
*Gene Product
*EcoGene number (EG)
*ECK number
*SWISS-PROT number
*Genbank number (gi)
*Blattner lab number (b)
*CGSC number
*Genomic Address
*Gene Description
| width='40%' |
*Primary Gene Name
*EG number
*ECK number
*b number
*Sequence
*Gene Name Mnemonic
*Alternate Gene Symbols
*Sequence
*Description
*Protein Sequence
*Protein length and MW
*Gene Quality
*Genomic Address (right end, left end, direction, and minute(%))
*EcoMap (10 kb neighbor genes)
*Link out
**Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
**ASAP
**CGSC
**GenoBase
**RegulonDB
**SWISS-PROT
**PDB Links
|-
|Title, author, or reference ID
|Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
|-
|Enzyme(s) and Genomic Adress
|Restriction Map
|}

'''Analysis'''

*Find the neighboring genes to the initially identified set
Yes. EcoMap (10 kb neighboring genes)
*Find/design primers for a certain gene
No.
*Find all the clones/KOs for those genes
Yes. Link to CGSC and GenoBase
*Find commonalities in function in the genes that are up or down-regulated in a given experiment
No.
*Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)
No.
*Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)
No.
*For a gene, segment of DNA, operon/regulons, pathway , find all the available information
No.

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

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
''This feature is not yet functional''
<ul><li>''$4$5'': [$2 <nowiki>$1</nowiki>]</li></ul>
=References=
Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

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

EcoGene

2006-06-21T03:41:58Z

Jiang7: /* Browsing */

'''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://ecogene.org {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

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

==Searching==
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

{| {{Prettytable}}
| width='25%' | '''Input'''
| width='40%' | '''Output'''
|-
| width='25%' |
*Gene Name (DNA, RNA, or pseudo gene)
*Synonym
*Gene Product
*EcoGene number (EG)
*ECK number
*SWISS-PROT number
*Genbank number (gi)
*Blattner lab number (b)
*CGSC number
*Genomic Address
*Gene Description
| width='40%' |
*Primary Gene Name
*EG number
*ECK number
*b number
*Sequence
*Gene Name Mnemonic
*Alternate Gene Symbols
*Sequence
*Description
*Protein Sequence
*Protein length and MW
*Gene Quality
*Genomic Address (right end, left end, direction, and minute(%))
*EcoMap (10 kb neighbor genes)
*Link out
**Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
**ASAP
**CGSC
**GenoBase
**RegulonDB
**SWISS-PROT
**PDB Links
|-
|Title, author, or reference ID
|Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
|-
|Enzyme(s) and Genomic Adress
|Restriction Map
|}

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

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
''This feature is not yet functional''
<ul><li>''$4$5'': [$2 <nowiki>$1</nowiki>]</li></ul>
=References=
Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

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

EcoGene

2006-06-21T03:40:35Z

Jiang7: /* Searching */

'''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://ecogene.org {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

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

'''Analysis'''

*Find the neighboring genes to the initially identified set
Yes. EcoMap (10 kb neighboring genes)
*Find/design primers for a certain gene
No.
*Find all the clones/KOs for those genes
Yes. Link to CGSC and GenoBase
*Find commonalities in function in the genes that are up or down-regulated in a given experiment
No.
*Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)
No.
*Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)
No.
*For a gene, segment of DNA, operon/regulons, pathway , find all the available information
No.

==Searching==
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

{| {{Prettytable}}
| width='25%' | '''Input'''
| width='40%' | '''Output'''
|-
| width='25%' |
*Gene Name (DNA, RNA, or pseudo gene)
*Synonym
*Gene Product
*EcoGene number (EG)
*ECK number
*SWISS-PROT number
*Genbank number (gi)
*Blattner lab number (b)
*CGSC number
*Genomic Address
*Gene Description
| width='40%' |
*Primary Gene Name
*EG number
*ECK number
*b number
*Sequence
*Gene Name Mnemonic
*Alternate Gene Symbols
*Sequence
*Description
*Protein Sequence
*Protein length and MW
*Gene Quality
*Genomic Address (right end, left end, direction, and minute(%))
*EcoMap (10 kb neighbor genes)
*Link out
**Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
**ASAP
**CGSC
**GenoBase
**RegulonDB
**SWISS-PROT
**PDB Links
|-
|Title, author, or reference ID
|Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
|-
|Enzyme(s) and Genomic Adress
|Restriction Map
|}

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

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
''This feature is not yet functional''
<ul><li>''$4$5'': [$2 <nowiki>$1</nowiki>]</li></ul>
=References=
Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

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

EcoGene

2006-06-21T03:37:14Z

Jiang7: /* Browsing */

'''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://ecogene.org {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

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

'''Analysis'''

*Find the neighboring genes to the initially identified set
Yes. EcoMap (10 kb neighboring genes)
*Find/design primers for a certain gene
No.
*Find all the clones/KOs for those genes
Yes. Link to CGSC and GenoBase
*Find commonalities in function in the genes that are up or down-regulated in a given experiment
No.
*Find genes with similar behavior across sets of different experiments (see Hughes et al 2000)
No.
*Given a gene name, find all the available info about this gene (motif, clones, mutants and relevant construction information, e.g., for making the mutants or the clones)
No.
*For a gene, segment of DNA, operon/regulons, pathway , find all the available information
No.

==Searching==
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

{| {{Prettytable}}
| width='25%' | '''Input'''
| width='40%' | '''Output'''
|-
| width='25%' |
*Gene Name (DNA, RNA, or pseudo gene)
*Synonym
*Gene Product
*EcoGene number (EG)
*ECK number
*SWISS-PROT number
*Genbank number (gi)
*Blattner lab number (b)
*CGSC number
*Genomic Address
*Gene Description
| width='40%' |
*Primary Gene Name
*EG number
*ECK number
*b number
*Sequence
*Gene Name Mnemonic
*Alternate Gene Symbols
*Sequence
*Description
*Protein Sequence
*Protein length and MW
*Gene Quality
*Genomic Address (right end, left end, direction, and minute(%))
*EcoMap (10 kb neighbor genes)
*Link out
**Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
**ASAP
**CGSC
**GenoBase
**RegulonDB
**SWISS-PROT
**PDB Links
|-
|Title, author, or reference ID
|Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
|-
|Enzyme(s) and Genomic Adress
|Restriction Map
|-

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

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
''This feature is not yet functional''
<ul><li>''$4$5'': [$2 <nowiki>$1</nowiki>]</li></ul>
=References=
Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

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

EcoGene

2006-06-21T03:25:32Z

Jiang7: /* Searching */

'''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://ecogene.org {{PAGENAME}}]
|-
| Updates
|
|-
| Upcoming events
| ''link to event calendar, if applicable''
|-
| Web Services
|
|}
=About {{PAGENAME}}=

Ecogene contains genomic and proteomic information about E.coli K12 MG1655.

=Using {{PAGENAME}}=
==Browsing==
==Searching==
Once you type in your gene of interest, Ecogene brings up several tidbits of information about that gene including, but not limited to synonyms and other identifiers, the gene name mnemonics (which are good to know), functions, and genomic location. Also, Ecogene also allows you to view other ORFs within a set distance from your gene. You can also get DNA and protein sequences and MW. A unique aspect of this database is that you also get a bibliography of the gene.

{| {{Prettytable}}
| width='25%' | '''Input'''
| width='40%' | '''Output'''
|-
| width='25%' |
*Gene Name (DNA, RNA, or pseudo gene)
*Synonym
*Gene Product
*EcoGene number (EG)
*ECK number
*SWISS-PROT number
*Genbank number (gi)
*Blattner lab number (b)
*CGSC number
*Genomic Address
*Gene Description
| width='40%' |
*Primary Gene Name
*EG number
*ECK number
*b number
*Sequence
*Gene Name Mnemonic
*Alternate Gene Symbols
*Sequence
*Description
*Protein Sequence
*Protein length and MW
*Gene Quality
*Genomic Address (right end, left end, direction, and minute(%))
*EcoMap (10 kb neighbor genes)
*Link out
**Resources (AmiGO, CMR, COG, ColiBASE, Colibri, Doodle, ECCE, ECDC, EchoBASE, EcoCyc, GenBank, GenExpDB, GenomeReviews, GenProtEC, GTOP, KEGG, ModBase, NiceZyme, pfam, ProDom, ProtoNet, SWISS-2D, TF Binding Sites, TIGR-CMR, TIGRHmm, Uniprot)
**ASAP
**CGSC
**GenoBase
**RegulonDB
**SWISS-PROT
**PDB Links
|-
|Title, author, or reference ID
|Title, authors, year, journal, vol, pages, Pudmed ID, Gene Links
|-
|Enzyme(s) and Genomic Adress
|Restriction Map
|-

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

=Other sites with related content=
=Technology=
==Web Services/API==
=Discussion=
==Trackbacks==
''This feature is not yet functional''
<ul><li>''$4$5'': [$2 <nowiki>$1</nowiki>]</li></ul>
=References=
Rudd, K.E., EcoGene: a genome sequence database for Escherichia coli K-12, Nucleic Acids Res., 28:60-64, 2000

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