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CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and...

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Autores principales: Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P., Chang, Yu-Chi, Madugundu, Anil K., Pandey, Akhilesh, Salzberg, Steven L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260756/
https://www.ncbi.nlm.nih.gov/pubmed/30486838
http://dx.doi.org/10.1186/s13059-018-1590-2
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author Pertea, Mihaela
Shumate, Alaina
Pertea, Geo
Varabyou, Ales
Breitwieser, Florian P.
Chang, Yu-Chi
Madugundu, Anil K.
Pandey, Akhilesh
Salzberg, Steven L.
author_facet Pertea, Mihaela
Shumate, Alaina
Pertea, Geo
Varabyou, Ales
Breitwieser, Florian P.
Chang, Yu-Chi
Madugundu, Anil K.
Pandey, Akhilesh
Salzberg, Steven L.
author_sort Pertea, Mihaela
collection PubMed
description We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and a total of 323,258 transcripts. These include 224 novel protein-coding genes and 116,156 novel transcripts. We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearly all of which are likely nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells. The CHESS database is available at http://ccb.jhu.edu/chess. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1590-2) contains supplementary material, which is available to authorized users.
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spelling pubmed-62607562018-12-10 CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise Pertea, Mihaela Shumate, Alaina Pertea, Geo Varabyou, Ales Breitwieser, Florian P. Chang, Yu-Chi Madugundu, Anil K. Pandey, Akhilesh Salzberg, Steven L. Genome Biol Database We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains 42,611 genes, of which 20,352 are potentially protein-coding and 22,259 are noncoding, and a total of 323,258 transcripts. These include 224 novel protein-coding genes and 116,156 novel transcripts. We detected over 30 million additional transcripts at more than 650,000 genomic loci, nearly all of which are likely nonfunctional, revealing a heretofore unappreciated amount of transcriptional noise in human cells. The CHESS database is available at http://ccb.jhu.edu/chess. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1590-2) contains supplementary material, which is available to authorized users. BioMed Central 2018-11-28 /pmc/articles/PMC6260756/ /pubmed/30486838 http://dx.doi.org/10.1186/s13059-018-1590-2 Text en © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Database
Pertea, Mihaela
Shumate, Alaina
Pertea, Geo
Varabyou, Ales
Breitwieser, Florian P.
Chang, Yu-Chi
Madugundu, Anil K.
Pandey, Akhilesh
Salzberg, Steven L.
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title_full CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title_fullStr CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title_full_unstemmed CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title_short CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
title_sort chess: a new human gene catalog curated from thousands of large-scale rna sequencing experiments reveals extensive transcriptional noise
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260756/
https://www.ncbi.nlm.nih.gov/pubmed/30486838
http://dx.doi.org/10.1186/s13059-018-1590-2
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