RNA sequencing integration into CellMiner and CellMiner CDB

CellMiner and CellMinerCDB  are web-based applications for mining publicly available genomic, molecular, and pharmacological datasets of human cancer cell lines including the NCI-60, Cancer Cell Line Encyclopedia (CCLE), Genomics of Drug Sensitivity in Cancer (GDSC), Cancer Therapeutics Response Portal (CTRP), NCI/DTP small cell lung cancer (SCLC), and NCI Almanac cell line sets.

Here NCI researchers introduce their RNA sequencing data for the NCI-60 and their access and integration with the other databases. Correlation to transcript microarray expression levels for identical genes and identical cell lines across CellMinerCDB demonstrate the high quality of these new RNA-seq data. They provide composite and isoform transcript expression data and demonstrate diversity in isoform composition for individual cancer- and pharmacologically relevant genes, including HRAS, PTEN, EGFR, RAD51, ALKBH2, BRCA1, ERBB2, TP53, FGFR2, and CTNND1. They reveal cell-specific differences in the overall levels of isoforms and show their linkage to expression of RNA processing and splicing genes as well as resultant alterations in cancer and pharmacological gene sets. Gene-drug pairings linked by pathways or functions show specific correlations to isoforms compared to composite gene expression, including ALKBH2-benzaldehyde, AKT3-vandetanib, BCR-imatinib, CDK1 and 20-palbociclib, CASP1-imexon, and FGFR3-pazopanib. Loss of MUC1 20 amino acid variable number tandem repeats, which is used to elicit immune response, and the presence of the androgen receptor AR-V4 and -V7 isoforms in all NCI-60 tissue of origin types demonstrates translational relevance.


In summary, the researchers introduce RNA-seq data to their CellMiner and CellMinerCDB web-applications, allowing their exploration for both research and translational purposes.

Availability – CellMiner – http://discover.nci.nih.gov/cellminer

CellMinerCDB – https://discover.nci.nih.gov/cellminercdb/

Reinhold WC, Varma S, Sunshine M, Elloumi F, Ofori-Atta K, Lee S, Trepel JB, Meltzer PS, Doroshow JH, Pommier Y. (2019) RNA sequencing of the NCI-60: Integration into CellMiner and CellMiner CDB. Cancer Res [Epub ahead of print]. [abstract]

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