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

Humans Phylogeny Proteins / genetics Genome, Human Algorithms Software Molecular Sequence Annotation

Journal

Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660

Informations de publication

Date de publication:
30 10 2023
Historique:
received: 21 12 2022
accepted: 16 10 2023
medline: 1 11 2023
pubmed: 31 10 2023
entrez: 31 10 2023
Statut: epublish

Résumé

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 .

Identifiants

DOI: 10.1186/s13059-023-03088-4 PMID: 37904256 PMC: PMC10614308
pubmed: 37904256
doi: 10.1186/s13059-023-03088-4
pii: 10.1186/s13059-023-03088-4
pmc: PMC10614308
doi:

Substances chimiques

Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

249

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG006677
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH123567
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM130151
Pays : United States

Informations de copyright

© 2023. The Author(s).

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Auteurs

Ales Varabyou (A)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. ales.varabyou@jhu.edu.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. ales.varabyou@jhu.edu.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. ales.varabyou@jhu.edu.
ORCID: 0000-0003-1060-7212

Markus J Sommer (MJ)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Beril Erdogdu (B)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Ida Shinder (I)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Cross Disciplinary Graduate Program in Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.

Ilia Minkin (I)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Kuan-Hao Chao (KH)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.

Sukhwan Park (S)

School of Biological Sciences, Seoul National University, Seoul, South Korea.
Artificial Intelligence Institute, Seoul National University, Seoul, South Korea.

Jakob Heinz (J)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Christopher Pockrandt (C)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Alaina Shumate (A)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Natalia Rincon (N)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Daniela Puiu (D)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.

Martin Steinegger (M)

School of Biological Sciences, Seoul National University, Seoul, South Korea.
Artificial Intelligence Institute, Seoul National University, Seoul, South Korea.
Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.

Steven L Salzberg (SL)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. salzberg@jhu.edu.
Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.

Mihaela Pertea (M)

Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. mpertea@jhu.edu.
Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. mpertea@jhu.edu.
Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. mpertea@jhu.edu.
Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. mpertea@jhu.edu.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › CHESS 3: an improved, comprehensive catalog of...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › CHESS 3: an improved, comprehensive catalog of...