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.