EcoliWiki - User contributions [en]

EcoliWiki:Wishlist

2008-05-15T17:27:53Z

Lee: Automatic retrieval of DOI links from MEDLINE/PubMed for all PMID pages

==Wishlist==
The EcoliWiki team strives to make the Wiki better. To that end, we are asking for your opinion. If there is a feature not currently available in EcoliWiki that you would like to see, describe it here.

===What's up and coming for EcoliWiki v2===
*Searching for information present in the tables specifically
*If I search for multiple genes in EcoliWiki, it would be nice for the output to be given in some delimited form.

===What we would like to see?===
*Search and type greek and non-English characters or some toolbar for it (lambda vs. the symbol, delta, sigma, etc.)
*Video clip upload
*Search for phenotype and output is a list of genes
*References- Pubmed Central IDs (for things w/o PMIDs)
*A "Go To" alphabet to organize the category pages
* RNAs in W3110
** links to RFAM
** pulldown menus for RNAs in Gbrowse
*synthetic lethal database[[User:Smrlab|Smrlab]]
*interactome data base[[User:Smrlab|Smrlab]]-Butland, Mori, other studies you had in mind
*CGSC Strain list
*Have the "edit toolbar" visible when editing tables
*List of Essential Genes
*Info on or list of compounds that can be taken up by coli e.g. cAMP?
*References- Automatic DOI's for ''all'' PMID articles. DOI's are available from PubMed/MEDLINE and hopefully can be automatically imported when the article abstract is imported. Prepending "<nowiki>http://dx.doi.org/</nowiki>" to a DOI gives a URL that takes the user directly to the journal's version of the online article. See, e.g, the Links section of the table on the [[PMID:17244358]] page.

PMID:17244358

2008-05-15T17:14:03Z

Lee: Added link to the article, via its DOI

{{RightTOC}}

<span style = 'font-size: large'> '''Carmack, CS, McCue, LA, Newberg, LA and Lawrence, CE''' (2007) PhyloScan: identification of transcription factor binding sites using cross-species evidence.''Algorithms Mol Biol'' '''2''':1</span>

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>BACKGROUND: When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statistically significant sites are revealed when a transcription factor binding site motif model is used to scan a genome-scale database. METHODS: We have developed a scanning algorithm, PhyloScan, which combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. The orthologous sequence data may be multiply aligned, unaligned, or a combination of aligned and unaligned. In aligned data, PhyloScan statistically accounts for the phylogenetic dependence of the species contributing data to the alignment and, in unaligned data, the evidence for sites is combined assuming phylogenetic independence of the species. The statistical significance of the gene predictions is calculated directly, without employing training sets. RESULTS: In a test of our methodology on synthetic data modeled on seven Enterobacteriales, four Vibrionales, and three Pasteurellales species, PhyloScan produces better sensitivity and specificity than MONKEY, an advanced scanning approach that also searches a genome for transcription factor binding sites using phylogenetic information. The application of the algorithm to real sequence data from seven Enterobacteriales species identifies novel Crp and PurR transcription factor binding sites, thus providing several new potential sites for these transcription factors. These sites enable targeted experimental validation and thus further delineation of the Crp and PurR regulons in E. coli. CONCLUSION: Better sensitivity and specificity can be achieved through a combination of (1) using mixed alignable and non-alignable sequence data and (2) combining evidence from multiple sites within an intergenic region.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17244358 PubMed] [http://dx.doi.org/10.1186/1748-7188-2-1 Article]
|}

==Significance {{HelpIcon|Help:Literature}} ==
You can scan for transcription factor binding sites in ''E. coli'' using the associated [http://bayesweb.wadsworth.org/cgi-bin/phylo_web.pl PhyloScan web server].

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='242070'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>

PMID:17244358

2008-05-15T16:49:00Z

Lee: Added link to associated web server

{{RightTOC}}

<span style = 'font-size: large'> '''Carmack, CS, McCue, LA, Newberg, LA and Lawrence, CE''' (2007) PhyloScan: identification of transcription factor binding sites using cross-species evidence.''Algorithms Mol Biol'' '''2''':1</span>

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>BACKGROUND: When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statistically significant sites are revealed when a transcription factor binding site motif model is used to scan a genome-scale database. METHODS: We have developed a scanning algorithm, PhyloScan, which combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. The orthologous sequence data may be multiply aligned, unaligned, or a combination of aligned and unaligned. In aligned data, PhyloScan statistically accounts for the phylogenetic dependence of the species contributing data to the alignment and, in unaligned data, the evidence for sites is combined assuming phylogenetic independence of the species. The statistical significance of the gene predictions is calculated directly, without employing training sets. RESULTS: In a test of our methodology on synthetic data modeled on seven Enterobacteriales, four Vibrionales, and three Pasteurellales species, PhyloScan produces better sensitivity and specificity than MONKEY, an advanced scanning approach that also searches a genome for transcription factor binding sites using phylogenetic information. The application of the algorithm to real sequence data from seven Enterobacteriales species identifies novel Crp and PurR transcription factor binding sites, thus providing several new potential sites for these transcription factors. These sites enable targeted experimental validation and thus further delineation of the Crp and PurR regulons in E. coli. CONCLUSION: Better sensitivity and specificity can be achieved through a combination of (1) using mixed alignable and non-alignable sequence data and (2) combining evidence from multiple sites within an intergenic region.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17244358 PubMed]
|}

==Significance {{HelpIcon|Help:Literature}} ==
You can scan for transcription factor binding sites in ''E. coli'' using the associated PhyloScan web server [http://bayesweb.wadsworth.org/cgi-bin/phylo_web.pl].

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='242070'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

==References==
{{RefHelp}}
<references/>