CHESS


37904256	CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. [PMID: 37904256] Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M. Abstract CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning techniques for noise filtering, and new protein structure prediction methods. CHESS 3 contains 41,356 genes, including 19,839 protein-coding genes and 158,377 transcripts, with 14,863 protein-coding transcripts not in other catalogs. It includes all MANE transcripts and at least one transcript for most RefSeq and GENCODE genes. On the CHM13 human genome, the CHESS 3 catalog contains an additional 129 protein-coding genes. CHESS 3 is available at http://ccb.jhu.edu/chess . Genome Biol. 2023:24(1) \| 10 Citations (from Europe PMC, 2025-03-15)
30486838	CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. [PMID: 30486838] Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL. Abstract 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 . Genome Biol. 2018:19(1) \| 152 Citations (from Europe PMC, 2025-03-15)

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. [PMID: 37904256]

Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M.

Abstract

CHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning techniques for noise filtering, and new protein structure prediction methods. CHESS 3 contains 41,356 genes, including 19,839 protein-coding genes and 158,377 transcripts, with 14,863 protein-coding transcripts not in other catalogs. It includes all MANE transcripts and at least one transcript for most RefSeq and GENCODE genes. On the CHM13 human genome, the CHESS 3 catalog contains an additional 129 protein-coding genes. CHESS 3 is available at http://ccb.jhu.edu/chess .

Genome Biol. 2023:24(1) | 10 Citations (from Europe PMC, 2025-03-15)

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. [PMID: 30486838]

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL.

Abstract

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 .

Genome Biol. 2018:19(1) | 152 Citations (from Europe PMC, 2025-03-15)

URL:	http://ccb.jhu.edu/chess
Full name:	comprehensive human expressed sequences
Description:	CHESS is a comprehensive set of human genes based on nearly 10,000 RNA sequencing experiments produced by the GTEx project. It includes a total of 19838 protein-coding genes and 17624 lncRNA genes. Adding antisense and other RNA genes, release v.3.0.1 of the database contains 63755 genes and 168451 transcripts. Of these transcripts, 99201 represent protein-coding gene isoforms and the rest are noncoding RNAs.
Year founded:	2018
Last update:	2023-04-27
Version:	v.3.0.1
Accessibility:	Accessible
Country/Region:	United States

Data type:	DNA Protein RNA
Data object:	Animal
Database category:	Gene genome and annotation
Major species:	Homo sapiens
Keywords:	protein-coding gene lncRNA gene

University/Institution:	Johns Hopkins University
Address:	Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
City:	Baltimore
Province/State:
Country/Region:	United States
Contact name (PI/Team):	Mihaela Pertea
Contact email (PI/Helpdesk):	mpertea@jhu.edu

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Database Commons a catalog of worldwide biological databases