Validation of transcription factor-to-cluster associations using ChIP-on-chip

Shown are five (TF,cluster) associations for which at least 30% of the genes within the cluster are represented on the tiling array, along with the results of the ChIP-on-chip assay for binding of the indicated TF to the promoters of genes within the indicated cluster. Column 1 indicates the transcription factor antibody target. Column 2 indicates the position-weight matrix that was used for scanning the promoters of genes in the cluster. Column 3 indicates the stimulus used. Column 4 indicates the gene cluster whose promoters the indicated TF is predicted to bind. Column 5 indicates the time points at which ChIP-on-chip assays were performed. Column 6 indicates the number of genes in the cluster. Column 7 indicates how many of these genes have probes tiled on the chip, in the flanking 5′ intergenic region (due to the much smaller microarray expression dataset used to select genes for the tiling array, only about 22% of the 1,960 differentially expressed genes were represented on the tiling array, as described in Materials and Methods). Column 8 indicates the number of these genes that were identified positively by ChIP-on-chip as having the indicated transcription factor bound to chromatin, in the 5′ flanking intergenic region. Column 9 indicates the P value for the enrichment of ChIP-on-chip hits among genes within the cluster identified by promoter scanning, as compared to the set of all genes on the array (Fisher's exact test). The ChIP-on-chip results for individual genes are provided in Table S13.