Figure 3

Integrating ChIP-Seq data with gene expression data. Methodology for integrating ChIP-Seq data with the time-course microarray gene expression data has been described here. The left hand panel describes the methodology for characterising the co-localised motifs. We have employed Spaced Motif Analysis (SPAMO) for characterising the set of motifs that were observed to occur together (P-value < 0.01). We have performed this analysis considering TRE and CRE as primary motifs. The right hand panel describes the methodology for predicting TF targets based upon gene expression data. We have used a modelling based approach for the short time-series, to rank the microarray genes based upon the likelihood of being targets of AP-1 family members, Jun/ATF. We then performed Gene Set Enrichment analysis to characterise over-representation of the transcripts containing peaks with SPAMO inferred interacting partners.