TFEA.ChIP is an R package in developement. Its purpose is to analyze transcription factor enrichment in a set of differentially expressed genes.
A web implementation of TFEA.ChIP is available at https://www.iib.uam.es/TFEA.ChIP/
Specifically TFEA.ChIP, uses information derived from the hundreds of ChIP-Seq experiments from the ENCODE Consortium[1] expanded to include additional datasets contributed to GEO database[2][3] by individual laboratories representing the binding sites of factors not assayed by ENCODE. The package includes a set of tools to customize the ChIP data, perform enrichment analysis and visualize the results. The package implements two enrichment analysis methods:
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Analysis of the association of TFBS and differential expression from 2x2 tables recording the presence of binding sites for a given TF in DE and control genes. The statistical significance of the association for each factor determined by a Fisher’s exact test.
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GSEA analysis, based on the core function of the GSEA algorithm for R[4][5], GSEA.EnrichmentScore.
1: ENCODE Project Consortium (2012) Nature 489, 57-74
2: Edgar, R et al. (2002) Nucleic Acids Res. 30:207-10
3: Barrett, T et al. (2013) Nucleic Acids Res. 41(Database issue):D991-5
4: Subramanian, Tamayo, et al. (2005) PNAS 102, 15545-15550
5: Mootha, Lindgren, et al. (2003) Nat Genet 34, 267-273