PT  - JOURNAL ARTICLE
AU  - Sneha Mitra
AU  - Anushua Biswas
AU  - Leelavati Narlikar
TI  - DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
AID  - 10.1101/122325
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 122325
4099  - http://biorxiv.org/content/early/2017/04/05/122325.short
4100  - http://biorxiv.org/content/early/2017/04/05/122325.full
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)