Distance-based assessment of the localization of functional annotations in 3D genome reconstructions.

ABSTRACT:

Background

Recent studies used the contact data or three-dimensional (3D) genome reconstructions from Hi-C (chromosome conformation capture with next-generation sequencing) to assess the co-localization of functional genomic annotations in the nucleus. These analyses dichotomized data point pairs belonging to a functional annotation as "close" or "far" based on some threshold and then tested for enrichment of "close" pairs. We propose an alternative approach that avoids dichotomization of the data and instead directly estimates the significance of distances within the 3D reconstruction.

Results

We applied this approach to 3D genome reconstructions for Plasmodium falciparum, the causative agent of malaria, and Saccharomyces cerevisiae and compared the results to previous appr

SUBMITTER: Capurso D 

PROVIDER: S-EPMC4254257 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature