RT Journal Article
SR Electronic
T1 DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 122325
DO 10.1101/122325
A1 Sneha Mitra
A1 Anushua Biswas
A1 Leelavati Narlikar
YR 2017
UL http://biorxiv.org/content/early/2017/04/05/122325.abstract
AB A high-throughput chromatin immunoprecipitation (ChIP) experiment is like a black-box: it reports all regions that are associated with the profiled protein based on the initial cross-linking step. These regions can be a highly diverse set of DNA sequences, with some making direct contact with the protein, some binding through intermediaries, and some being a result of long-range interactions involving the protein. We present diversity, a method that identifies the distinct components of such a mixture, leaving no data behind, while at the same time, using no prior motif knowledge. Using the example of the REST protein, we show that these different components give insights into the various complexes that may be forming along the chromatin and their regulatory functions.http://diversity.ncl.res.in/ (webserver)https://github.com/NarlikarLab/DIVERSITY (standalone for Mac OSX/Linux)