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

Qing Zhou, Hiram Chipperfield, Douglas Melton and Wing Hung Wong

Supplementary Notes

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.

Table 7 Target genes and CRMs of the Nanog-bound activator regions.

Table 8 Target genes and CRMs of the Phc1-bound repressed regions.

Table 9 CRMs in the upstream of the Phc1-bound repressed genes.

Supplementary Figures

Figure 4 Histograms of the (A) positive and (B) negative fold change genes in the Oct4-sorted series.

Figure 5 Overlaps between the genes defined in various expression profiles and the TF-bound genes.

Figure 6 Expression profiles of the ligands and receptors in the Notch pathway in (A) the Oct4-sorted and (B) the RA-induction series.

Figure 7 Motifs of the 15 core regulators in Table 1.

Supplementary Datasets

Dataset 1 The complete expression profiles of the Oct4-sorted series.

Dataset 2 Oct4-sorted+ gene list.

Dataset 3 Oct4-sorted− gene list.

Dataset 4 Expression profiles of the Oct4Ri+ genes.

Dataset 5 Expression profiles of the Oct4Ri− genes.

Dataset 6 Expression profiles of the RA+ genes.

Dataset 7 Expression profiles of the RA− genes.

Dataset 8 Refseq genes associated with the Oct4-bound regions.

Dataset 9 Refseq genes associated with the Nanog-bound regions.

Dataset 10 Refseq genes associated with the Phc1-bound regions.

Raw data of the Oct4-sorted series (CEL files) Download