Fig. 2

Effect of randomly selected genes on functional enrichments. a Effect of randomly selected genes on functional enrichments using DNase-DGF data. Transcriptional target genes were predicted using DNase-DGF data in human monocytes, CD4⁺ T, CD20⁺ B, other four somatic and two stem cells (H1-hESC and iPSC) (see also Additional file 1: Figure S1). To test whether slight changes of transcriptional target genes were reflected in the normalized number of their functional enrichments, the ratio of randomly selected genes in the target genes of each TF was changed between 5% and 60%. In the left part of the graphs, randomly selected genes were replaced with the target genes where the total number of target genes was unchanged. In the right part of the graphs, randomly selected genes were added to the target genes where the total number of target genes was increased. The result of Gene Ontology annotation was shown. The results of Pathway Commons and KEGG were shown in Additional file 1: Figure S1. Native target genes showed the most functional enrichments in most cell types. b Effect of randomly selected genes on functional enrichments using ChIP-seq data. Transcriptional target genes were predicted using ChIP-seq data of 19 TF in H1-hESC. The results of nine functional annotation databases were shown and the result of target genes of microRNAs was shown in Additional file 1: Figure S2. Native target genes showed the most functional enrichments using most annotation databases except for low frequent functional annotations. Putative transcriptional target genes tend to include similar function of genes