BINOCh: binding inference from nucleosome occupancy changes

Bioinformatics
Clifford A MeyerX Shirley Liu

Abstract

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

References

Dec 11, 1999·Nucleic Acids Research·E WingenderF Schacherer
Dec 19, 2003·Nucleic Acids Research·Albin SandelinBoris Lenhard
Oct 3, 2006·Nature Genetics·Jason S CarrollMyles Brown
Mar 9, 2010·Nature Genetics·Housheng Hansen HeX Shirley Liu

Citations

Apr 18, 2012·Genome Research·Housheng Hansen HeX Shirley Liu
Nov 7, 2012·Molecular and Cellular Biology·Michael P VerziRamesh A Shivdasani
Aug 24, 2011·Genome Biology·Tao LiuX Shirley Liu
Dec 9, 2014·Biomedical Papers of the Medical Faculty of the University Palacký, Olomouc, Czechoslovakia·Hana JaneckovaTomas Adam
Sep 29, 2015·Briefings in Bioinformatics·Vladimir B Teif
Nov 22, 2018·Nucleic Acids Research·Rongbin ZhengX Shirley Liu
Mar 1, 2013·Quantitative Biology·Hyunjin ShinX Shirley Liu

Related Concepts

Histone H7
Polynucleosomes
Androgen Receptor
Computer Programs and Programming
Dihydroepitestosterone
Transcription Factor
Cdna Microarrays
Cell Line, Tumor
Cell Differentiation Process
Histones

Related Feeds

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.