GeSICA: genome segmentation from intra-chromosomal associations.

ABSTRACT:

Background

Various aspects of genome organization have been explored based on data from distinct technologies, including histone modification ChIP-Seq, 3C, and its derivatives. Recently developed Hi-C techniques enable the genome wide mapping of DNA interactomes, thereby providing the opportunity to study genome organization in detail, but these methods also pose challenges in methodology development.

Results

We developed Genome Segmentation from Intra Chromosomal Associations, or GeSICA, to explore genome organization and applied the method to Hi-C data in human GM06990 and K562 cells. GeSICA calculates a simple logged ratio to efficiently segment the human genome into regions with two distinct states that correspond to rich and poor functional element states. Inside the ri

SUBMITTER: Liu L 

PROVIDER: S-EPMC3460730 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature