The Cancer Genome Atlas (TCGA) project has generated a very large, public collection of multiple types of ‘omic’ data on samples from >10,000 cancer patients, across 33 different tumor types. Of particular interest to cancer researchers are the alternate splicing changes in tumor cells that may represent a return to developmental splicing patterns of metabolism, angiogenesis, mobility and proliferation ( 2, 3). The splicing mechanism enables a single gene to produce multiple protein products, and changes in splicing patterns are closely associated with development and differentiation.
TCGA SpliceSeq is freely available for academic, government or commercial use.Īlternative mRNA splicing is a regulated process that occurs in nearly all multi-exon human genes ( 1). Splicing data can also be downloaded for inclusion in integrative analyses. The interface presents intuitive graphical representations of splicing patterns, read counts and various statistical summaries, including percent spliced in. Investigators can interrogate genes of interest, search for the genes that show the strongest variation between or among selected tumor types, or explore splicing pattern changes between tumor and adjacent normal samples. Percent Spliced In (PSI) values for splice events on samples from 33 different tumor types, including available adjacent normal samples, have been loaded into TCGA SpliceSeq. TCGA SpliceSeq ( ) is a web-based resource that provides a quick, user-friendly, highly visual interface for exploring the alternative splicing patterns of TCGA tumors.
Aberrant splicing patterns in cancers have been implicated in such processes as carcinogenesis, de-differentiation and metastasis. RNASeq technology, combined with computational tools like our SpliceSeq package, provides a comprehensive, detailed view of alternative mRNA splicing. TCGA's RNASeq data represent one of the largest collections of cancer transcriptomes ever assembled.
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