Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors

We present a pipeline for inferring biological functions regulated by a combinatorial interaction of transcription factors. Using a robust statistical method the pipeline intersects the presence of transcription factor binding sites in gene upstream sequences with Gene Ontology terms associated with these genes. Positional frequency matrices for the transcription factors constitute the input of the pipeline and significantly enriched biological processes are reported as the output. We demonstrate the usage of the pipeline using two groups of transcription factors: a cell-cycle related family of E2F factors and a NFAT/AP-1 pair involved in immune response. In both cases the reported results match well the experimental knowledge. Furthermore, for the NFAT/AP-1 composite element novel functions are predicted.

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