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bioRxiv · 10.1101/036012

Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems

Le Shu·Yuqi Zhao·Zeyneb Kurt·Sean Geoffrey Byars·Taru Tukiainen·Johannes Kettunen·Samuli Ripatti·Bin Zhang·Michael Inouye·Ville-Petteri Makinen·Xia Yang
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Abstract

Mergeomics is a computational pipeline (http://mergeomics.research.idre.ucla.edu/Download/Package/) that integrates multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It first identifies biological pathways and tissue-specific gene subnetworks that are perturbed by disease-associated molecular entities. The disease-associated subnetworks are then projected onto tissue-specific gene-gene interaction networks to identify local hubs as potential key drivers of pathological perturbations. The pipeline is modular and can be applied across species and platform boundaries, and uniquely conducts pathway/network level meta-analysis of multiple genomic studies of various data types. Application of Mergeomics to cholesterol datasets revealed novel regulators of cholesterol metabolism.

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Le Shu, Yuqi Zhao, Zeyneb Kurt, Sean Geoffrey Byars, Taru Tukiainen, Johannes Kettunen, Samuli Ripatti, Bin Zhang, Michael Inouye, Ville-Petteri Makinen, Xia Yang. 2016-01-07. Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems. https://doi.org/10.1101/036012

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