Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines

Barry R. Zeeberg, William Reinhold, René Snajder, Gerhard G. Thallinger, John N. Weinstein, Kurt W. Kohn, Yves Pommier

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background: The NCI-60 is a panel of 60 diverse human cancer cell lines used by the U.S. National Cancer Institute to screen compounds for anticancer activity. In the current study, gene expression levels from five platforms were integrated to yield a single composite transcriptome profile. The comprehensive and reliable nature of that dataset allows us to study gene co-expression across cancer cell lines. Methodology/Principal Findings: Hierarchical clustering revealed numerous clusters of genes in which the genes co-vary across the NCI-60. To determine functional categorization associated with each cluster, we used the Gene Ontology (GO) Consortium database and the GoMiner tool. GO maps genes to hierarchically-organized biological process categories. GoMiner can leverage GO to perform ontological analyses of gene expression studies, generating a list of significant functional categories. Conclusions/Significance: GoMiner analysis revealed many clusters of coregulated genes that are associated with functional groupings of GO biological process categories. Notably, those categories arising from coherent co-expression groupings reflect cancer-related themes such as adhesion, cell migration, RNA splicing, immune response and signal transduction. Thus, these clusters demonstrate transcriptional coregulation of functionally-related genes.

Original languageEnglish (US)
Article numbere30317
JournalPloS one
Volume7
Issue number1
DOIs
StatePublished - Jan 24 2012

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Gene Ontology
Multigene Family
multigene family
Genes
Cells
cell lines
Biological Phenomena
Cell Line
Gene Expression
Neoplasms
genes
Ontology
RNA Splicing
National Cancer Institute (U.S.)
Transcriptome
Cell Movement
Cluster Analysis
Signal Transduction
Gene expression
Databases

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines. / Zeeberg, Barry R.; Reinhold, William; Snajder, René; Thallinger, Gerhard G.; Weinstein, John N.; Kohn, Kurt W.; Pommier, Yves.

In: PloS one, Vol. 7, No. 1, e30317, 24.01.2012.

Research output: Contribution to journalArticle

Zeeberg, Barry R. ; Reinhold, William ; Snajder, René ; Thallinger, Gerhard G. ; Weinstein, John N. ; Kohn, Kurt W. ; Pommier, Yves. / Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines. In: PloS one. 2012 ; Vol. 7, No. 1.
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