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Genome Biol. 2015 Sep 21;16:198. doi: 10.1186/s13059-015-0767-1.

HiCPlotter integrates genomic data with interaction matrices.

Author information

1
Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. kcakedemir@mdanderson.org.
2
Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. lchin@mdanderson.org.
3
Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. lchin@mdanderson.org.

Abstract

Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or the presence of architectural proteins have been implicated in regulation and assembly of the chromatin architecture. Therefore, comprehensive visualization of this multi-faceted structure is important to unravel the connections between nuclear architecture and transcriptional regulation. Here, we present an easy-to-use open-source visualization tool, HiCPlotter, to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. https://github.com/kcakdemir/HiCPlotter.

PMID:
26392354
PMCID:
PMC4576377
DOI:
10.1186/s13059-015-0767-1
[Indexed for MEDLINE]
Free PMC Article

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