Issues in Omics Data Integration for Gene Set Analysis and Aberrant Pathway Identification


Correspondence to: Michael F. Ochs, Department of Oncology, Johns Hopkins University, 550 North Broadway, Suite 1101, Baltimore, MD 21205, USA.



Preclinical Research

The impact of omics technologies, from microarrays to next-generation sequencing, on drug development has been limited by our inability to integrate the data meaningfully for pathway analysis. Here we discuss the relationship between biomolecules and pathway activity, focusing on metabolic and signaling pathways. We discuss how each type of pathway requires a different approach to the generation of pathway statistics from omics data and provide guidance for the creation of appropriate gene sets for pathway analysis.