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

Daniel R. Rhodes, Shanker Kalyana-Sundaram, Vasudeva Mahavisno, Radhika Varambally, Jianjun Yu, Benjamin B. Briggs, Terrence R. Barrette, Matthew J. Anstet, Colleen Kincead-Beal, Prakash Kulkarni, Sooryanaryana Varambally, Debashis Ghoshy, Arul M. Chinnaiyan

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)166-180
Number of pages15
JournalNeoplasia
Volume9
Issue number2
DOIs
StatePublished - Feb 2007
Externally publishedYes

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Gene Regulatory Networks
Neoplasm Genes
Transcriptome
Neoplasms
Gene Expression Profiling
Microarray Analysis
Oligonucleotide Array Sequence Analysis
Computational Biology
Biomedical Research
Databases
Gene Expression

Keywords

  • Bioinformatics
  • Cancer gene expression
  • Differential expression
  • Microarrays
  • Oncomine

ASJC Scopus subject areas

  • Cancer Research

Cite this

Rhodes, D. R., Kalyana-Sundaram, S., Mahavisno, V., Varambally, R., Yu, J., Briggs, B. B., ... Chinnaiyan, A. M. (2007). Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia, 9(2), 166-180. https://doi.org/10.1593/neo.07112

Oncomine 3.0 : Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. / Rhodes, Daniel R.; Kalyana-Sundaram, Shanker; Mahavisno, Vasudeva; Varambally, Radhika; Yu, Jianjun; Briggs, Benjamin B.; Barrette, Terrence R.; Anstet, Matthew J.; Kincead-Beal, Colleen; Kulkarni, Prakash; Varambally, Sooryanaryana; Ghoshy, Debashis; Chinnaiyan, Arul M.

In: Neoplasia, Vol. 9, No. 2, 02.2007, p. 166-180.

Research output: Contribution to journalArticle

Rhodes, DR, Kalyana-Sundaram, S, Mahavisno, V, Varambally, R, Yu, J, Briggs, BB, Barrette, TR, Anstet, MJ, Kincead-Beal, C, Kulkarni, P, Varambally, S, Ghoshy, D & Chinnaiyan, AM 2007, 'Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles', Neoplasia, vol. 9, no. 2, pp. 166-180. https://doi.org/10.1593/neo.07112
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB et al. Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007 Feb;9(2):166-180. https://doi.org/10.1593/neo.07112
Rhodes, Daniel R. ; Kalyana-Sundaram, Shanker ; Mahavisno, Vasudeva ; Varambally, Radhika ; Yu, Jianjun ; Briggs, Benjamin B. ; Barrette, Terrence R. ; Anstet, Matthew J. ; Kincead-Beal, Colleen ; Kulkarni, Prakash ; Varambally, Sooryanaryana ; Ghoshy, Debashis ; Chinnaiyan, Arul M. / Oncomine 3.0 : Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. In: Neoplasia. 2007 ; Vol. 9, No. 2. pp. 166-180.
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