Figure 2

Conservation and re-use of TFos. (A) The distribution of SeqCons, FunctActive, and FunctCons regulatory elements summarized for all human mouse analogous cell lines (Additional file 1: Table S2). In both cell lines, a small fraction of mappable regulatory elements is FunctCons (33% and 15% cell average for human and mouse respectively). A larger fraction (46% and 50% cell average for human and mouse respectively) is FunctActive (plots for each cell are in Additional file 1: Figures S15, S16). (B) Loss and gain of TF binding sites. We used TFos in our data to discover TF binding sites (TFBS) on both species. We mapped human (respectively mouse) TFBS to mouse (respectively human) and computed their distance to the closest mouse (respectively human) TFBS of the same TF on an analogous cell. Among these TFBS those with a positive distance but less than 150 bp contribute to the corresponding bar in the human (respectively mouse) subplot. In other words, each bar is the count of TFBS that were lost and gained within a 150 bp window of the original site. (C) Reuse of FunctActive TFos between different cells and factors. A point on the scatterplot indicates the number of TFos of the corresponding assay in the reference species that can be classified as FunctCons or FunctActive when considering a fixed size set of randomly chosen assays in the comparison species. We performed multiple computations for each chosen size of such sets. Lines indicate the accumulated number of FunctCons, FunctActive, and Seqcons TFos. In this figure, about 93% of the (Mel, Max) assay is covered by TFos from just 35% of the query assays (plots for other cells/TFs in Additional file 1: Figures S17, S18).