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Nucleic Acids Res. 2016 Jan 4;44(D1):D1018-22. doi: 10.1093/nar/gkv1288. Epub 2015 Nov 23.

TCGASpliceSeq a compendium of alternative mRNA splicing in cancer.

Author information

1
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA In Silico Solutions, Falls Church, VA 22043, USA mryan@insilico.us.com.
2
In Silico Solutions, Falls Church, VA 22043, USA.
3
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
4
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Abstract

TCGA's RNASeq data represent one of the largest collections of cancer transcriptomes ever assembled. RNASeq technology, combined with computational tools like our SpliceSeq package, provides a comprehensive, detailed view of alternative mRNA splicing. Aberrant splicing patterns in cancers have been implicated in such processes as carcinogenesis, de-differentiation and metastasis. TCGA SpliceSeq (http://bioinformatics.mdanderson.org/TCGASpliceSeq) is a web-based resource that provides a quick, user-friendly, highly visual interface for exploring the alternative splicing patterns of TCGA tumors. 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. 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. The interface presents intuitive graphical representations of splicing patterns, read counts and various statistical summaries, including percent spliced in. Splicing data can also be downloaded for inclusion in integrative analyses. TCGA SpliceSeq is freely available for academic, government or commercial use.

PMID:
26602693
PMCID:
PMC4702910
DOI:
10.1093/nar/gkv1288
[Indexed for MEDLINE]
Free PMC Article

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