PMID:17244358 - Revision history

imported>Wikientrybot: change PMID template to TableEdit version

2013-09-15T04:31:04Z

change PMID template to TableEdit version

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	!align=left \|Citation		!align=left \|Citation
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	'''~~No author listed~~''' (2007) PhyloScan: identification of transcription factor binding sites using cross-species evidence. ''Algorithms Mol Biol'' '''2''':1		'''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
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	!align=left \|Abstract		!align=left \|Abstract

imported>Wikientrybot: replace GO_table_reference with annotationlinks

2013-09-01T18:55:53Z

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 ==Annotations {{HelpIcon|Help:Literature}}==
-<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1-->
+<protect><annotationlinks/></protect>
 ==EcoliWiki Links {{HelpIcon|Help:Literature}} ==

imported>Wikientrybot: change PMID template to TableEdit version

2013-09-01T18:55:53Z

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-|{{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>
+!align=left  |Citation
 |-
-|{{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]
+!align=left  |Keywords
 |}
+<!--box uid=d41d8cd98f00b204e9800998ecf8427e.134454.X52238db946dcf-->
 ==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].

127.0.0.1: /Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

2010-06-17T20:36:04Z

/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

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	{\| id="R482c685e3dae1" class=" tableEdit GO_table_reference"		{\| id="R482c685e3dae1" class=" tableEdit GO_table_reference"
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	!\|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status		!\|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

127.0.0.1: Update TableEdit tables.

2010-01-09T04:28:15Z

Update TableEdit tables.

← Older revision		Revision as of 04:28, 9 January 2010
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	!\|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status		!\|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

	\|-class=~~'sortbottom'~~		\|- class="tableEdit_footer"
	\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] \|\| \|\| \|\| \|\| \|\| \|\| \|\| \|\|		\|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table]</span> \|\| \|\| \|\| \|\| \|\| \|\| \|\| \|\|
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imported>Wikientrybot: Fix links due to TableEditLinks.php changes.

2009-02-20T03:43:02Z

Fix links due to TableEditLinks.php changes.

← Older revision		Revision as of 03:43, 20 February 2009
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	!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status		!\|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

	\|-class='sortbottom'		\|-class='sortbottom'
	\|[{{SERVER}}{{SCRIPTPATH}}~~/index.php~~?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}} edit table] \|\| \|\| \|\| \|\| \|\| \|\| \|\| \|\|		\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.R482c685e3dae1&page=0&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] \|\| \|\| \|\| \|\| \|\| \|\| \|\| \|\|
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Lee: Added link to the article, via its DOI

2008-05-15T17:14:03Z

Added link to the article, via its DOI

← Older revision		Revision as of 17:14, 15 May 2008
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	\|{{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}} \|'''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>
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	\|{{TableHeadingColor}} nowrap \|'''Links''' \|\| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17244358 PubMed]		\|{{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}} ==		==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].		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}}==		== Useful Materials and Methods {{HelpIcon\|Help:Literature}}==

Lee: Added link to associated web server

2008-05-15T16:49:00Z

Added link to associated web server

← Older revision		Revision as of 16:49, 15 May 2008
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	==Significance {{HelpIcon\|Help:Literature}} ==		==Significance {{HelpIcon\|Help:Literature}} ==
	~~{{LitSignificance}}~~		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}}==		== Useful Materials and Methods {{HelpIcon\|Help:Literature}}==

Lee: New PMID: Page!

2008-05-15T16:44:15Z

New PMID: Page!

New page

{{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}} ==
{{LitSignificance}}

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

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

{|class = 'sortable' {{Prettytable}} id='242070'
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!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
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</protect>

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

==See also==

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