Coherent Functional Modules Improve Transcription Factor Target Identification, Cooperativity Prediction, and Disease Association
(A): A TF is associated to a module if its targets are significantly enriched in a particular module. TF are connected to their targets using ChIP-Seq data, which may (solid) or may not (dashed) be contained with an expression module. GO annotations (colored blue/yellow) are used in enrichment analysis to associate modules and their factors to functional pathways. (B): We evaluated the quality of TFICA derived TF targets based on the hypothesis that if a TF does regulate a target, then it is more likely that the TF and the target will share a functional annotation. Across ChIP-Seq scores, TFICA outperforms the naive method, and this performance is further increased when only considering high and medium-confidence modules (see text).