title: ONCOMINE: a cancer microarray database and integrated data-mining platform.
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.
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Rhodes
authors.forename: Jianjun
authors.initials: J
authors.lastname: Yu
authors.forename: K
authors.initials: K
authors.lastname: Shanker
authors.forename: Nandan
authors.initials: N
authors.lastname: Deshpande
authors.forename: Radhika
authors.initials: R
authors.lastname: Varambally
authors.forename: Debashis
authors.initials: D
authors.lastname: Ghosh
authors.forename: Terrence
authors.initials: T
authors.lastname: Barrette
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Pandey
authors.forename: Arul M
authors.initials: AM
authors.lastname: Chinnaiyan
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D009369:Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software