Spot validation. This figure demonstrates CHANCE's spot validation module. H3K4me3 in H1 HESCs from the Broad ENCODE data is spot validated for promoter regions of known housekeeping and tissue-specific genes. (a) The summary statement gives the IP over Input fold-change in read count as well as a P-value based on a Poisson null model (see Materials and methods). A random locus is added for comparison. The putative proximal promoter was estimated to 3 kbp upstream to 3 kbp downstream of the transcription start site. (b) Graphical representation of the results. On the x-axis, we have the gene symbols followed by the tissue type with which their expression is commonly identified; HK denotes 'house keeping' or ubiquitously expressed genes. The y-axis shows the number of reads mapping to the corresponding promoter region, both in IP and Input.
Diaz et al. Genome Biology 2012 13:R98 doi:10.1186/gb-2012-13-10-r98