Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.

ABSTRACT: Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the

SUBMITTER: Mourad R 

PROVIDER: S-EPMC4874696 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature