title: Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America. zeebergb@mail.nih.gov
authors.forename: Barry R
authors.initials: BR
authors.lastname: Zeeberg
authors.forename: William
authors.initials: W
authors.lastname: Reinhold
authors.forename: René
authors.initials: R
authors.lastname: Snajder
authors.forename: Gerhard G
authors.initials: GG
authors.lastname: Thallinger
authors.forename: John N
authors.initials: JN
authors.lastname: Weinstein
authors.forename: Kurt W
authors.initials: KW
authors.lastname: Kohn
authors.forename: Yves
authors.initials: Y
authors.lastname: Pommier
mesh_terms: D000465:Algorithms; D000970:Antineoplastic Agents / Q000302:isolation & purification / Q000494:pharmacology; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004353:Drug Evaluation, Preclinical / Q000379:methods; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks / Q000502:physiology*; D056726:Genetic Association Studies; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D005810:Multigene Family / Q000235:genetics* / Q000502:physiology*; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology
chemical_list: D000970:Antineoplastic Agents