For example, the top 200 bound motif-words are responsible for 4,006 binding events in the human genome; in fact, just 2,492 words (3.6% of the possible words) account for over half of the binding events in the human genome.
Human TF binding events in CRMs and singletons were categorized by the number of species they were shared in and then associated with the nearest gene.
We show median normalized ChIP signals ((sum(ChIP +1)/(sum(Input)+1))∗n, where n is total(ChIP /total(Input)) before and after CTCF knockdown 1 kb around the CTCF summit at five-way shared and human-only binding events in Figure S1.
Furthermore, we confirmed that ERα binding events in E2-regulated MammaPrint genes are also found in 2 ER-positive Luminal human breast tumor samples, for which ERα ChIP-seq data are available (Fig. 3a).
Analysis of the MBD DNA binding isotherms clearly shows two binding events in sequence.
For example, repeat-associated binding sites accounted for 11.1% and 28.3% of all CTCF-binding events in genomes of human and mouse ESCs, respectively (Kunarso et al. 2010).
We observed an increase in shared binding events between human, mouse, and dog with motif lengths from CEBPA (4%), to HNF4A (5%), to CTCF (24%), but we did not see a significant dependence when looking at a collection of sequence-specific factors.
Interestingly, a majority of the LINE- and LTR-embedded human-specific TF-binding events in hESCs are represented by the retrotransposons L1PA2 (196 events), L1HS (64), LTR7 (109), and LTR5_HS (81) that are transcriptionally active in human cells (supplementary fig. S1, Supplementary Material online).
We define a set of tissue-invariant sites as binding events present in the human ENCODE cell lines Gm19238, Gm19239, H1hesc, HeLA, Huvec, K562, MCF-7, and Progfib.
The effects of cisplatin on cytochrome c conformation were recently studied by HDX MS. Other metal-binding events in proteins were investigated by HDX MS including zinc binding to β-2-microglobulin and the related analyses of porphyrin binding to human ferrochelatase.
