Oncomine 3.0: Genes, Pathways, and Networks in a Collection of 18,000 Cancer Gene Expression Profiles

TLDR

Cancer transcriptome microarray data are widely generated but largely inaccessible and analytic methods are limited. The authors created Oncomine to collect, standardize, analyze, and deliver cancer transcriptome data, and they update the initiative with database and analysis modules and key observations. Oncomine aggregates 18,000 microarray profiles, standardizes them, and provides analysis modules for pathway and network interrogation. The analysis identified deregulated genes, pathways, and networks across 18,000 microarrays covering most cancer types, and the results are available online.

Abstract

DNA microarrays have been widely applied to cancer transcriptome analysis; however, the majority of such data are not easily accessible or comparable. Furthermore, several important analytic approaches have been applied to microarray analysis; however, their application is often limited. To overcome these limitations, we have developed Oncomine, a bioinformatics initiative aimed at collecting, standardizing, analyzing, and delivering cancer transcriptome data to the biomedical research community. Our analysis has identified the genes, pathways, and networks deregulated across 18,000 cancer gene expression microarrays, spanning the majority of cancer types and subtypes. Here, we provide an update on the initiative, describe the database and analysis modules, and highlight several notable observations. Results from this comprehensive analysis are available at http://www.oncomine.org.