title: Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.
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.
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-0940, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Rhodes
authors.forename: Shanker
authors.initials: S
authors.lastname: Kalyana-Sundaram
authors.forename: Vasudeva
authors.initials: V
authors.lastname: Mahavisno
authors.forename: Radhika
authors.initials: R
authors.lastname: Varambally
authors.forename: Jianjun
authors.initials: J
authors.lastname: Yu
authors.forename: Benjamin B
authors.initials: BB
authors.lastname: Briggs
authors.forename: Terrence R
authors.initials: TR
authors.lastname: Barrette
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Anstet
authors.forename: Colleen
authors.initials: C
authors.lastname: Kincead-Beal
authors.forename: Prakash
authors.initials: P
authors.lastname: Kulkarni
authors.forename: Sooryanaryana
authors.initials: S
authors.lastname: Varambally
authors.forename: Debashis
authors.initials: D
authors.lastname: Ghosh
authors.forename: Arul M
authors.initials: AM
authors.lastname: Chinnaiyan
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics; D019295:Computational Biology / Q000458:organization & administration*; D003625:Data Collection; D003626:Data Display; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D015195:Drug Design; D001330:Electronic Data Processing; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D006801:Humans; D020407:Internet; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000235:genetics*; D009369:Neoplasms / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D013382:Subtraction Technique; D014158:Transcription, Genetic
chemical_list: D000970:Antineoplastic Agents; D009363:Neoplasm Proteins