ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform

TLDR

DNA microarray technology has generated vast oncogenomic data revealing complex cancer gene expression patterns, yet the lack of a unified bioinformatic resource keeps most of this information stagnant and underused. ONCOMINE is a web‑based cancer microarray database and data‑mining platform designed to enable discovery from genome‑wide expression analyses. The platform aggregates 65 datasets with nearly 48 million measurements from over 4,700 microarray experiments, offers differential expression, subtype, and clinical/pathology analyses, and allows gene‑level querying, visualization, and annotation‑filtered biomarker discovery.

Abstract

DNA microarray technology has led to an explosion of oncogenomic analyses, generating a wealth of data and uncovering the complex gene expression patterns of cancer. Unfortunately, due to the lack of a unifying bioinformatic resource, the majority of these data sit stagnant and disjointed following publication, massively underutilized by the cancer research community. Here, we present ONCOMINE, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses. To date, ONCOMINE contains 65 gene expression datasets comprising nearly 48 million gene expression measurements form over 4700 microarray experiments. Differential expression analyses comparing most major types of cancer with respective normal tissues as well as a variety of cancer subtypes and clinical-based and pathology-based analyses are available for exploration. Data can be queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets.