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BINOCh: binding inference from nucleosome occupancy changes.

ABSTRACT:

Unlabelled

Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biologists to use such data to infer the identity of key transcription factors that regulate the response of a cell to a stimulus or determine a program of differentiation.

Availability

The BINOCh open source Python package is freely available at http://liulab.dfci.harvard.edu/BINOCh under the FreeBSD license.

SUBMITTER: Meyer CA

PROVIDER: S-EPMC3117357 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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BINOCh: binding inference from nucleosome occupancy changes.

Meyer Clifford A CA He Housheng H HH Brown Myles M Liu X Shirley XS

Bioinformatics (Oxford, England) 20110505 13

<h4>Unlabelled</h4>Transcription factor binding events are frequently associated with a pattern of nucleosome occupancy changes in which nucleosomes flanking the binding site increase in occupancy, while those in the vicinity of the binding site itself are displaced. Genome-wide information on enhancer proximal nucleosome occupancy can be readily acquired using ChIP-seq targeting enhancer-related histone modifications such as H3K4me2. Here, we present a software package, BINOCh that allows biolo ...[more]

PMID: 21551136

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