A Gene Regulatory Network in Mouse Embryonic Stem Cells ( Supplementary Information )

Supplementary Tables Table 2 Compiled list of motifs for cis-regulatory analyses. Table 3 Significance and enrichment of the compiled motifs in various ChIP-bound and associated regions. Table 4 Expanded regulatory network of 337 genes expressed in ESC. The regulators for each gene are indicated by 1s in the table. Table 5 Regulatory interactions for the top ranking putative target genes activated by the network. Table 6 Target genes and CRMs of the Oct4-bound activator regions. In the table, “EffLen” is the total length of the ChIP-regions associated with a gene after masking out repeats. “TFcount” and “TFscore” are the number of scanned sites and their total log-probability ratio scores. “Scanpval”, “ChIPpval”, and “Combpval” refer to the p-values of the enrichment of scanned sites, of total ChIP-intensity, and the combined p-value, respectively. Table 7 Target genes and CRMs of the Nanog-bound activator regions. The column names are defined similarly to those in Table 6. Table 8 Target genes and CRMs of the Phc1-bound repressed regions. The column names are defined similarly to those in Table 6. Table 9 CRMs in the upstream of the Phc1-bound repressed genes. The column names are defined similarly to those in Table 6.