TY - JOUR
T1 - TCGASpliceSeq a compendium of alternative mRNA splicing in cancer
AU - Ryan, Michael
AU - Wong, Wing Chung
AU - Brown, Robert
AU - Akbani, Rehan
AU - Su, Xiaoping
AU - Broom, Bradley
AU - Melott, James
AU - Weinstein, John
N1 - Funding Information:
U.S. National Cancer Institute (NCI; MD Anderson TCGA Genome Data Analysis Center) [CA143883, CA083639]; Cancer Prevention Research Institute of Texas (CPRIT) [RP130397]; Mary K. Chapman Foundation, the Michael & Susan Dell Foundation (honoring Lorraine Dell); MD Anderson Cancer Center Support Grant P30 CA016672 (the Bioinformatics Shared Resource). Funding for open access charge: Mary K. Chapman Foundation.
Publisher Copyright:
© The Author(s) 2015.
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
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U2 - 10.1093/nar/gkv1288
DO - 10.1093/nar/gkv1288
M3 - Article
C2 - 26602693
AN - SCOPUS:84976878595
SN - 0305-1048
VL - 44
SP - D1018-D1022
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -