Supplementary Figure 10: Analysis of transcription factor binding sites in network gene loci.
(a) Motifs for DNA-binding TFs in the core network. Note that Eto2 and Lmo2 do not bind directly to the DNA, and the binding site of the Notch partner Rbpj was used for Notch1 as described previously. (b) To search for evidence that predicted regulatory interactions are direct, all haematopoietic TF ChIP-seq data in Codex2 were searched for peaks within the gene body or 50 kb up- and down-stream of the 20 network genes. Overlapping peaks were merged to identify putative regulatory sequences. Different colours indicate peaks from different experiments. A transcription factor binding site search (TFBS) was performed using TFBSsearch3 on the mouse genomic sequence of all regions to identify the consensus binding sites of the network TFs. Evolutionary conservation of TF binding motifs is a well-recognised feature of truly functional binding sites4. To identify conserved binding sites, PhyloP scores were calculated for each motif across 60 species using the tool provided by the UCSC Genome Browser. Evolutionarily conserved motifs previously validated in functional assays by us and other were characterised by PhyloP scores greater than 1, which was therefore used as the threshold. Results are summarised in Supplementary Table 2.
