TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
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Cites methods from "TRANSFAC® and its module TRANSCompe..."
...PWMs from TRANSFAC and JASPAR were used to scan the promoters of all human genes in the region −2000 and +500 from the transcription factor start site (TSS)....
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...These six libraries include the ability to identify transcription factors that are enriched for target genes within the input list using four different options: 1) ChEA [10]; 2) position weight matrices (PWMs) from TRANSFAC [11] and JASPAR [12]; 3) target genes generated from PMWs downloaded from the UCSC genome browser [13]; and 4) transcription factor targets extracted from the ENCODE project [14,15]....
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...Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, et al: TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes....
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...Table visualization of the Enrichr results showing the top 10 enriched terms in the TRANSFAC and JASPAR PWMs gene-set library....
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4,128 citations
Cites background from "TRANSFAC® and its module TRANSCompe..."
...Contact: gsea@broadinstitute.org Received on January 13, 2011; revised on April 4, 2011; accepted on April 12, 2011...
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References
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"TRANSFAC® and its module TRANSCompe..." refers methods in this paper
...From the databases integrated by InterPro, Pfam (19) and SMART (20), as well as PROSITE (21) models corresponding to low-complexity regions are selected....
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