Cell type–specific TF binding and collective TF binding. (A) An example of ChIP-seq signals of the TF KLF4 and MYC in mouse ESCs and MEF cells, showing that the same TF binds to different genomic sites in different cell types. The bars in the genome tracks are the called peaks. (B) Numbers of total ChIP-seq peaks of KLF4 and MYC in ESCs and MEF cells and their overlaps between the two cells. (C) The number of TF ChIP-seq peaks that are unique to one cell type or are shared by two, three, four, and five different cell types, which are K562, HepG2, GM12878, H1-hESC, and HeLa-S3. (OL) Overlap or shared. There is no YY1 or SP1 ChIP-seq data in HeLa-S3, so the comparisons of YY1 and SP1 are only among four cell lines. (D) An example of the collective TF binding and cell type–specific binding of KLF4 and MYC in mouse ESCs and MEF cells. (E) When peaks from different TFs overlap with each other, we merged them into one peak. (F) The total ChIP-seq peaks of all the TFs and the merged peaks as the number of TFs increases, in mouse ESCs and MEF cells. (G) An analysis similar to what is presented in F, in K562 and HepG2 cell lines. (H) The number of total TF peaks and merged peaks in the five different cell lines.
