TCGA Gene Expression Datasets

Abstract:

The Cancer Genome Atlas (TCGA) was a large-scale collaborative project initiated by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI). It aimed to comprehensively characterize the genomic and molecular landscape of various cancer types. These datasets contain gene expression profiles of bladder urothelial carcinoma (BLCA), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), glioblastoma multiforme (GBM), head & neck squamous cell carcinoma (HNSC), kidney renal clear cell carcinoma (KIRC), and lower grade glioma (LGG).

The gene expression profiles for BLCA, CESC, HNSC, KIRC, and LGG were measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the University of North Carolina TCGA genome characterization center.  The gene expression profile of the GBM dataset was measured experimentally using the Affymetrix HT Human Genome U133a microarray platform by the Broad Institute of MIT and Harvard University cancer genomic characterization center.

Inspiration:

This dataset was uploaded to UBRITE for GTKB project. 

Instruction:

The log2(x+1) normalization was removed, and z-normalization was performed on the BLCA, CESC, HNSC, KIRC, and LGG datasets.

The log2(x) normalization was removed, and z-normalization was performed on the GBM dataset.

Acknowledgments:

Goldman, M.J., Craft, B., Hastie, M. et al. Visualizing and interpreting cancer genomics data via the Xena platform. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0546-8.

The Cancer Genome Atlas Research Network., Weinstein, J., Collisson, E. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45, 1113–1120 (2013). https://doi.org/10.1038/ng.2764.

U-BRITE last update: 07/13/2023