Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.

By Daniel R. Rhodes, Shanker Kalyana-Sundaram, Vasudeva Mahavisno, Radhika Varambally, Jianjun Yu, Benjamin B Briggs, T. Barrette, Matthew J Anstet, Colleen Kincead-Beal, Prakash Kulkarni and 3 more. Neoplasia, 2007

2,055 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3e24ff6f5f8eba407effc09a3e23ee583d4ee0e7

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Citations in the corpus

Comprehensive literature review and statistical considerations for microarray meta-analysis (2012, background): “…(92) and Gene Age Nexus (93)], Pancreatic Expression database (94), COXPRESdb for gene networks in mammals (95), CYCLONET for cell cycle regulation (96), HCNet for heart and calcium functional network (14), and general cancer databases [Oncomine (97) and Cancer Genome Workbench (CGWB) (98)].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, methodology): “The Oncomine resource includes more than 18,000 gene expression profiles (http://oncomine.org; Rhodes et al., 2007a).”
SIRT3 is a Mitochondrial Localized Tumor Suppressor Required for Maintenance of Mitochondrial Integrity and Metabolism During Stress (2010, methodology): “The Oncomine cancer microarray database (Rhodes et al., 2007) was subsequently used to determine if SIRT3 expression is decreased in human malignancies.”
UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses (2017, methodology): “Oncomine [35,36] provides an interactive platform for gene expression profiling, using TCGA and other published cDNA, Affymetrix, and Illumina microarray data.”