Concordance of Gene Expression and Functional Correlation Patterns across the NCl-60 Cell Lines and the Cancer Genome Atlas Glioblastoma Samples

Background: The NCl-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 NCl-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 NCl-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 NCl-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. Conclusion: Many of the gene-gene correlations found in the NCl-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 NCl-60 and GBM data sets, but there are others that occur only in NCl-60 or only in GBM. In sum, this analysis provides an additional perspective on both the utility and the limitations of the NCl-60 in furthering our understanding of cancers in vivo.