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PLoS Comput Biol. 2017 Jun 15;13(6):e1005586. doi: 10.1371/journal.pcbi.1005586. eCollection 2017 Jun.

GINOM: A statistical framework for assessing interval overlap of multiple genomic features.

Author information

1
Naval Surface Warfare Center Panama City Division, Panama City, Florida, United States of America.
2
Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America.
3
Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America.
4
Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island, United States of America.
5
Department of Statistics, Florida State University, Tallahassee, Florida, United States of America.

Abstract

A common problem in genomics is to test for associations between two or more genomic features, typically represented as intervals interspersed across the genome. Existing methodologies can test for significant pairwise associations between two genomic intervals; however, they cannot test for associations involving multiple sets of intervals. This limits our ability to uncover more complex, yet biologically important associations between multiple sets of genomic features. We introduce GINOM (Genomic INterval Overlap Model), a new method that enables testing of significant associations between multiple genomic features. We demonstrate GINOM's ability to identify higher-order associations with both simulated and real data. In particular, we used GINOM to explore L1 retrotransposable element insertion bias in lung cancer and found a significant pairwise association between L1 insertions and heterochromatic marks. Unlike other methods, GINOM also detected an association between L1 insertions and gene bodies marked by a facultative heterochromatic mark, which could explain the observed bias for L1 insertions towards cancer-associated genes.

PMID:
28617797
PMCID:
PMC5491313
DOI:
10.1371/journal.pcbi.1005586
[Indexed for MEDLINE]
Free PMC Article

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