oPOSSUM: integrated tools for analysis of regulatory motif over-representation

被引：125

作者：

Sui, Shannan J. Ho ^{[1
,2
]}

Fulton, Debra L. ^{[1
,2
]}

Arenillas, David J. ^{[1
,3
]}

Kwon, Andrew T. ^{[1
,2
]}

Wasserman, Wyeth W. ^{[1
,3
]}

机构：

[1] Univ British Columbia, Child & Family Res Inst, Ctr Mol Med & Therapeut, Vancouver, BC V5Z 1M9, Canada

[2] Univ British Columbia, Grad Program Genet, Vancouver, BC V5Z 1M9, Canada

[3] Univ British Columbia, Dept Med Genet, Vancouver, BC V5Z 1M9, Canada

来源：

NUCLEIC ACIDS RESEARCH | 2007年 / 35卷

基金：

加拿大健康研究院;

关键词：

D O I：

10.1093/nar/gkm427

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 [生物化学与分子生物学]; 081704 [应用化学];

摘要：

The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/.

引用

页码：W245 / W252

页数：8

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