title: Concordance of gene expression and functional correlation patterns across the NCI-60 cell lines and the Cancer Genome Atlas glioblastoma samples.
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. We recently clustered genes based on correlation of expression profiles across the NCI-60. Many of the resulting clusters were characterized by cancer-associated biological functions. The set of curated glioblastoma (GBM) gene expression data from the Cancer Genome Atlas (TCGA) initiative has recently become available. Thus, we are now able to determine which of the processes are robustly shared by both the immortalized cell lines and clinical cancers.
  
  
  RESULTS
  Our central observation is that some sets of highly correlated genes in the NCI-60 expression data are also highly correlated in the GBM expression data. Furthermore, a "double fishing" strategy identified many sets of genes that show Pearson correlation ≥0.60 in both the NCI-60 and the GBM data sets relative to a given "bait" gene. The number of such gene sets far exceeds the number expected by chance.
  
  
  CONCLUSIONS
  Many of the gene-gene correlations found in the NCI-60 do not reflect just the conditions of cell lines in culture; rather, they reflect processes and gene networks that also function in vivo. A number of gene network correlations co-occur in the NCI-60 and GBM data sets, but there are others that occur only in NCI-60 or only in GBM. In sum, this analysis provides an additional perspective on both the utility and the limitations of the NCI-60 in furthering our understanding of cancers in vivo.
authors: 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: Barry R
authors: BR
authors: Zeeberg
authors: Kurt W
authors: KW
authors: Kohn
authors: Ari
authors: A
authors: Kahn
authors: Vladimir
authors: V
authors: Larionov
authors: John N
authors: JN
authors: Weinstein
authors: William
authors: W
authors: Reinhold
authors: Yves
authors: Y
authors: Pommier
mesh_terms: D045744:Cell Line, Tumor; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D052138:Genes, Neoplasm; D015894:Genome, Human; D005909:Glioblastoma / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D054547:National Cancer Institute (U.S.); D014481:United States