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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
12
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pubmed:dateCreated |
2010-11-30
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pubmed:abstractText |
Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. MISO also detects differentially regulated exons or isoforms. Application of MISO implicated the RNA splicing factor hnRNP H1 in the regulation of alternative cleavage and polyadenylation, a role that was supported by UV cross-linking-immunoprecipitation sequencing (CLIP-seq) analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-11944992,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-14980514,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-15956978,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-16171461,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-18337823,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-18516045,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-18566288,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-18978772,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-18978789,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19010929,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19208812,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19239895,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19244387,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19448617,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19506027,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19703394,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-19749754,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-20044349,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-20436462,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-20436464,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-20459815,
http://linkedlifedata.com/resource/pubmed/commentcorrection/21057496-20835245
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Dec
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pubmed:issn |
1548-7105
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
7
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
1009-15
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pubmed:dateRevised |
2011-7-25
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pubmed:meshHeading |
pubmed-meshheading:21057496-Alternative Splicing,
pubmed-meshheading:21057496-Base Sequence,
pubmed-meshheading:21057496-DNA-Binding Proteins,
pubmed-meshheading:21057496-Exons,
pubmed-meshheading:21057496-Heterogeneous-Nuclear Ribonucleoproteins,
pubmed-meshheading:21057496-Humans,
pubmed-meshheading:21057496-Introns,
pubmed-meshheading:21057496-NFATC Transcription Factors,
pubmed-meshheading:21057496-Protein Isoforms,
pubmed-meshheading:21057496-RNA,
pubmed-meshheading:21057496-RNA, Messenger,
pubmed-meshheading:21057496-Reverse Transcriptase Polymerase Chain Reaction,
pubmed-meshheading:21057496-Sequence Analysis, RNA
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pubmed:year |
2010
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pubmed:articleTitle |
Analysis and design of RNA sequencing experiments for identifying isoform regulation.
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pubmed:affiliation |
Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.,
Research Support, Non-U.S. Gov't
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