Figure 1

A random sampling model of determination of TF binding avidity potential on the genome defined in a ChIP-seq experiment. Sequencing TFBS-enriched DNA fragments can be assayed to determine the specific clusters of DNA sequences bound by TF protein. Results are strongly depended from the number of read (sample size). A: Small sample size. B: Large sample size. Blue horizontal stake: specific DNA fragment; white horizontal stake: non-specific DNA fragment forming non-specific (false-positive) clusters. C: BS1-BS6 are binding loci presented in the given cells: blue vertical stakes are relative binding avidity in the loci; BS6 might be modified (epigenetically) and suppressed BS (a stake with triangle basis) and therefore it might be not detected in ChIp-seq assay. BS1 and BS4 might be not detected in the assay due to sample size limit. D: A scheme of the random Markov process of binding-dissociation of TF-DNA realized on the genome scale. The graph illustrates concept of birth-death random process model utilized in this work (see Methods).