PT  - JOURNAL ARTICLE
AU  - Le Shu
AU  - Yuqi Zhao
AU  - Zeyneb Kurt
AU  - Sean Geoffrey Byars
AU  - Taru Tukiainen
AU  - Johannes Kettunen
AU  - Samuli Ripatti
AU  - Bin Zhang
AU  - Michael Inouye
AU  - Ville-Petteri Mäkinen
AU  - Xia Yang
TI  - Mergeomics: integration of diverse genomics resources to identify pathogenic perturbations to biological systems
AID  - 10.1101/036012
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 036012
4099  - http://biorxiv.org/content/early/2016/01/07/036012.short
4100  - http://biorxiv.org/content/early/2016/01/07/036012.full
AB  - 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.