Human cancer long non-coding RNA transcriptomes
Once thought to be a part of the 'dark matter' of the genome, long non-coding RNAs (lncRNAs) are emerging as an integral functional component of the mammalian transcriptome. LncRNAs are a novel class of mRNA-like transcripts which, despite no known protein-coding potential, demonstrate a w...
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| creator | Gibb, Ewan A Vucic, Emily A Enfield, Katey S S Stewart, Greg L Lonergan, Kim M Kennett, Jennifer Y Becker-Santos, Daiana D MacAulay, Calum E Lam, Stephen Brown, Carolyn J Lam, Wan L |
| description | Once thought to be a part of the 'dark matter' of the genome, long non-coding RNAs (lncRNAs) are emerging as an integral functional component of the mammalian transcriptome. LncRNAs are a novel class of mRNA-like transcripts which, despite no known protein-coding potential, demonstrate a wide range of structural and functional roles in cellular biology. However, the magnitude of the contribution of lncRNA expression to normal human tissues and cancers has not been investigated in a comprehensive manner. In this study, we compiled 272 human serial analysis of gene expression (SAGE) libraries to delineate lncRNA transcription patterns across a broad spectrum of normal human tissues and cancers. Using a novel lncRNA discovery pipeline we parsed over 24 million SAGE tags and report lncRNA expression profiles across a panel of 26 different normal human tissues and 19 human cancers. Our findings show extensive, tissue-specific lncRNA expression in normal tissues and highly aberrant lncRNA expression in human cancers. Here, we present a first generation atlas for lncRNA profiling in cancer. |
| doi_str_mv | 10.1371/journal.pone.0025915 |
| format | Article |
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Here, we present a first generation atlas for lncRNA profiling in cancer.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0025915</identifier><identifier>PMID: 21991387</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aberration ; Analysis ; Biology ; Cancer ; Cellular structure ; Chromosomes, Human - genetics ; Dark matter ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Library ; Genes ; Genome, Human - genetics ; Genomes ; Genomics ; Human tissues ; Humans ; Interdisciplinary aspects ; Laboratories ; Leukemia ; Lymphoma ; Lymphomas ; Medicine ; Metastasis ; Mutation ; Neoplasms - genetics ; Non-coding RNA ; Oncology ; Organ Specificity - genetics ; Pathology ; Pediatrics ; Proteins ; Ribonucleic acid ; RNA ; RNA, Untranslated - genetics ; RNA, Untranslated - metabolism ; Serial analysis of gene expression ; Structure-function relationships ; Tissues ; Transcription ; Transcription (Genetics) ; Transcriptome ; Tumors</subject><ispartof>PloS one, 2011-10, Vol.6 (10), p.e25915-e25915</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Gibb et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Gibb et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c723t-91c6f38e00366b4b41265b58026c5f93430f34e00ce530bce73a7a91d0542a683</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185064/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185064/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21991387$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gibb, Ewan A</creatorcontrib><creatorcontrib>Vucic, Emily A</creatorcontrib><creatorcontrib>Enfield, Katey S S</creatorcontrib><creatorcontrib>Stewart, Greg L</creatorcontrib><creatorcontrib>Lonergan, Kim M</creatorcontrib><creatorcontrib>Kennett, Jennifer Y</creatorcontrib><creatorcontrib>Becker-Santos, Daiana D</creatorcontrib><creatorcontrib>MacAulay, Calum E</creatorcontrib><creatorcontrib>Lam, Stephen</creatorcontrib><creatorcontrib>Brown, Carolyn J</creatorcontrib><creatorcontrib>Lam, Wan L</creatorcontrib><title>Human cancer long non-coding RNA transcriptomes</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Once thought to be a part of the 'dark matter' of the genome, long non-coding RNAs (lncRNAs) are emerging as an integral functional component of the mammalian transcriptome. 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Here, we present a first generation atlas for lncRNA profiling in cancer.</description><subject>Aberration</subject><subject>Analysis</subject><subject>Biology</subject><subject>Cancer</subject><subject>Cellular structure</subject><subject>Chromosomes, Human - genetics</subject><subject>Dark matter</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Gene Library</subject><subject>Genes</subject><subject>Genome, Human - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Human tissues</subject><subject>Humans</subject><subject>Interdisciplinary aspects</subject><subject>Laboratories</subject><subject>Leukemia</subject><subject>Lymphoma</subject><subject>Lymphomas</subject><subject>Medicine</subject><subject>Metastasis</subject><subject>Mutation</subject><subject>Neoplasms - genetics</subject><subject>Non-coding RNA</subject><subject>Oncology</subject><subject>Organ Specificity - genetics</subject><subject>Pathology</subject><subject>Pediatrics</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Untranslated - genetics</subject><subject>RNA, Untranslated - metabolism</subject><subject>Serial analysis of gene expression</subject><subject>Structure-function relationships</subject><subject>Tissues</subject><subject>Transcription</subject><subject>Transcription (Genetics)</subject><subject>Transcriptome</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk11rFDEUhgdRbF39B6ILguLFbpOcJJPcCEtRu1As1I_bkMlkdlNmkjWZEf33Zt1p2ZGCkouE5DnvyfkqiucYLTGU-OwmDNHrdrkL3i4RIkxi9qA4xRLIghMED4_OJ8WTlG4QYiA4f1ycECwlBlGeFmcXQ6f93GhvbJy3wW_mPviFCbXLx-tPq3kftU8mul0fOpueFo8a3Sb7bNxnxdcP77-cXywurz6uz1eXC1MS6BcSG96AsAgB5xWtKCacVUwgwg1rJFBADdD8bCwDVBlbgi61xDVilGguYFa8POju2pDUGGtSGJAkhHEJmVgfiDroG7WLrtPxlwraqT8XIW6Ujr0zrVXaVrQkdS05F5RnfwCVAMy1ILqhjGatd6O3oepsbazPUbcT0emLd1u1CT8UYMEQ3wu8GQVi-D7Y1KvOJWPbVnsbhqQk4UJSIPBPUkiBS4ly4mbFq7_I-9MwUhudI3W-CfmDZq-pVrTkIjO0zNTyHiqv2nbO5A5qXL6fGLydGGSmtz_7jR5SUuvP1__PXn2bsq-P2K3Vbb9NoR16F3yagvQAmhhSira5qwZGaj8At9lQ-wFQ4wBksxfHlbwzuu14-A2QWfyO</recordid><startdate>20111003</startdate><enddate>20111003</enddate><creator>Gibb, Ewan A</creator><creator>Vucic, Emily A</creator><creator>Enfield, Katey S S</creator><creator>Stewart, Greg L</creator><creator>Lonergan, Kim M</creator><creator>Kennett, Jennifer Y</creator><creator>Becker-Santos, Daiana D</creator><creator>MacAulay, Calum E</creator><creator>Lam, Stephen</creator><creator>Brown, Carolyn J</creator><creator>Lam, Wan L</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20111003</creationdate><title>Human cancer long non-coding RNA transcriptomes</title><author>Gibb, Ewan A ; Vucic, Emily A ; Enfield, Katey S S ; Stewart, Greg L ; Lonergan, Kim M ; Kennett, Jennifer Y ; Becker-Santos, Daiana D ; MacAulay, Calum E ; Lam, Stephen ; Brown, Carolyn J ; Lam, Wan L</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c723t-91c6f38e00366b4b41265b58026c5f93430f34e00ce530bce73a7a91d0542a683</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Aberration</topic><topic>Analysis</topic><topic>Biology</topic><topic>Cancer</topic><topic>Cellular structure</topic><topic>Chromosomes, Human - 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| subjects | Aberration Analysis Biology Cancer Cellular structure Chromosomes, Human - genetics Dark matter Gene expression Gene Expression Profiling Gene Expression Regulation, Neoplastic Gene Library Genes Genome, Human - genetics Genomes Genomics Human tissues Humans Interdisciplinary aspects Laboratories Leukemia Lymphoma Lymphomas Medicine Metastasis Mutation Neoplasms - genetics Non-coding RNA Oncology Organ Specificity - genetics Pathology Pediatrics Proteins Ribonucleic acid RNA RNA, Untranslated - genetics RNA, Untranslated - metabolism Serial analysis of gene expression Structure-function relationships Tissues Transcription Transcription (Genetics) Transcriptome Tumors |
| title | Human cancer long non-coding RNA transcriptomes |
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