Figure 5

Screening of candidate genes that may be controlled at the level of RNA degradation from the ENCODE dataset. (a) Number of candidate genes screened from the indicated cell types based on the ENCODE data. (b) Gene ontology (GO) enrichment of genes in the ChIP (+) / RNA (−) regions in the indicated cell types based on the ENCODE data. ChIP-seq signal intensities were comparable between different cell types, although RNA-seq-based gene expression values were remarkably different. The GO term enrichment with the lowest P-value for each cell line is shown. (c, d) Enriched consensus transcription factor binding sites for genes in the ChIP (+) / RNA (−) region for ENCODE dataset. (c) Graphical representation of the enriched consensus binding sites in the promoter regions of the genes in ChIP (+) / RNA (−) region for ENCODE dataset. (d) The list of cell lines with consensus binding site enrichment from the TRANSFAC database. (e) The nuclear/cytoplasmic gene expression values for the genes where RNA half-life may be the contributor to the RNA levels and all other genes in H1 human embryonic stem cells (hesc). Statistical significance of the difference is indicated under the x-axis.