Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of mul...
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Veröffentlicht in: | Nature genetics 2008-12, Vol.40 (12), p.1413-1415 |
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description | We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of multiexon genes undergo alternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels. |
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New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of multiexon genes undergo alternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.</description><identifier>ISSN: 1061-4036</identifier><identifier>EISSN: 1546-1718</identifier><identifier>DOI: 10.1038/ng.259</identifier><identifier>PMID: 18978789</identifier><identifier>CODEN: NGENEC</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>Agriculture ; Alternative Splicing ; Animal Genetics and Genomics ; Biological and medical sciences ; Biomedical and Life Sciences ; Biomedicine ; Brain ; brief-communication ; Cancer Research ; DNA microarrays ; DNA sequencing ; Estimates ; Fundamental and applied biological sciences. Psychology ; Gene expression ; Gene Expression Profiling ; Gene Function ; Genetic engineering ; Genetics of eukaryotes. Biological and molecular evolution ; Human Genetics ; Humans ; Medical research ; Messenger RNA ; Methods ; Nucleotide sequencing ; Physiological aspects ; RNA Splice Sites ; RNA, Messenger ; Sequence Analysis, RNA - methods ; Studies ; Tissues</subject><ispartof>Nature genetics, 2008-12, Vol.40 (12), p.1413-1415</ispartof><rights>Springer Nature America, Inc. 2008</rights><rights>2009 INIST-CNRS</rights><rights>COPYRIGHT 2008 Nature Publishing Group</rights><rights>Copyright Nature Publishing Group Dec 2008</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c619t-4a70df4d3faf0e6dd8cf97e670695eca73452be6f7615eb52b542c30321daebe3</citedby><cites>FETCH-LOGICAL-c619t-4a70df4d3faf0e6dd8cf97e670695eca73452be6f7615eb52b542c30321daebe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,781,785,2728,27926,27927</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=20942147$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18978789$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Blencowe, Benjamin J</creatorcontrib><creatorcontrib>Pan, Qun</creatorcontrib><creatorcontrib>Shai, Ofer</creatorcontrib><creatorcontrib>Lee, Leo J</creatorcontrib><creatorcontrib>Frey, Brendan J</creatorcontrib><title>Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing</title><title>Nature genetics</title><addtitle>Nat Genet</addtitle><addtitle>Nat Genet</addtitle><description>We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of multiexon genes undergo alternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.</description><subject>Agriculture</subject><subject>Alternative Splicing</subject><subject>Animal Genetics and Genomics</subject><subject>Biological and medical sciences</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Brain</subject><subject>brief-communication</subject><subject>Cancer Research</subject><subject>DNA microarrays</subject><subject>DNA sequencing</subject><subject>Estimates</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Function</subject><subject>Genetic engineering</subject><subject>Genetics of eukaryotes. 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Biological and molecular evolution</topic><topic>Human Genetics</topic><topic>Humans</topic><topic>Medical research</topic><topic>Messenger RNA</topic><topic>Methods</topic><topic>Nucleotide sequencing</topic><topic>Physiological aspects</topic><topic>RNA Splice Sites</topic><topic>RNA, Messenger</topic><topic>Sequence Analysis, RNA - methods</topic><topic>Studies</topic><topic>Tissues</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Blencowe, Benjamin J</creatorcontrib><creatorcontrib>Pan, Qun</creatorcontrib><creatorcontrib>Shai, Ofer</creatorcontrib><creatorcontrib>Lee, Leo J</creatorcontrib><creatorcontrib>Frey, Brendan J</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Nature genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Blencowe, Benjamin J</au><au>Pan, Qun</au><au>Shai, Ofer</au><au>Lee, Leo J</au><au>Frey, Brendan J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing</atitle><jtitle>Nature genetics</jtitle><stitle>Nat Genet</stitle><addtitle>Nat Genet</addtitle><date>2008-12-01</date><risdate>2008</risdate><volume>40</volume><issue>12</issue><spage>1413</spage><epage>1415</epage><pages>1413-1415</pages><issn>1061-4036</issn><eissn>1546-1718</eissn><coden>NGENEC</coden><abstract>We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. 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subjects | Agriculture Alternative Splicing Animal Genetics and Genomics Biological and medical sciences Biomedical and Life Sciences Biomedicine Brain brief-communication Cancer Research DNA microarrays DNA sequencing Estimates Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling Gene Function Genetic engineering Genetics of eukaryotes. Biological and molecular evolution Human Genetics Humans Medical research Messenger RNA Methods Nucleotide sequencing Physiological aspects RNA Splice Sites RNA, Messenger Sequence Analysis, RNA - methods Studies Tissues |
title | Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing |
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