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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...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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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. |
format | Online Article Text |
id | pubmed-6260756 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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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