Figure 3

GSE Spatial Visualizer snapshots showing illustrative examples of ChIP-chip and ChIP-PET data for (a) OCT4 and (b) NANOG. The fold enrichment for a single ChIP-chip replicate (for OCT4 or NANOG) is shown against the genomic coordinate scale for the gene (in base pairs). The grey boxes represent the locations of 'bound regions' from each of the factor's three ChIP-chip replicates. The white boxes show the overlapping ChIP-PET reads for the displayed region. A 'bound region' in ChIP-PET experiments had four or more overlapping reads in OCT4, and three or more overlapping reads in the case of NANOG. Gene exons and introns are represented by pink boxes and solid horizontal lines, respectively. For each visualized gene, the transcriptional start site, direction of transcription and RefSeq annotation derived from the UCSC database are also specified.