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

Ales Varabyou; Markus J Sommer; Beril Erdogdu; Ida Shinder; Ilia Minkin; Kuan-Hao Chao; Sukhwan Park; Jakob Heinz; Christopher Pockrandt; Alaina Shumate; Natalia Rincon; Daniela Puiu; Martin Steinegger; Steven L Salzberg; Mihaela Pertea

doi:10.1186/s13059-023-03088-4

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

Genome Biol. 2023 Oct 30;24(1):249. doi: 10.1186/s13059-023-03088-4.

Authors

Ales Varabyou^{1

2

3}, Markus J Sommer^{4

5}, Beril Erdogdu^{4

5}, Ida Shinder^{4

6}, Ilia Minkin^{4

5}, Kuan-Hao Chao^{4

7}, Sukhwan Park^{8

9}, Jakob Heinz^{4

5}, Christopher Pockrandt^{4

5}, Alaina Shumate^{4

5}, Natalia Rincon^{4

5}, Daniela Puiu^{4

5}, Martin Steinegger^{8

9

10}, Steven L Salzberg^{11

12

13

14

15}, Mihaela Pertea^{16

17

18

19}

Affiliations

¹ Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. [email protected].
² Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. [email protected].
³ Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. [email protected].
⁴ Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
⁵ Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA.
⁶ Cross Disciplinary Graduate Program in Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
⁷ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁸ School of Biological Sciences, Seoul National University, Seoul, South Korea.
⁹ Artificial Intelligence Institute, Seoul National University, Seoul, South Korea.
¹⁰ Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
¹¹ Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. [email protected].
¹² Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. [email protected].
¹³ Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. [email protected].
¹⁴ Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. [email protected].
¹⁵ Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA. [email protected].
¹⁶ Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA. [email protected].
¹⁷ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. [email protected].
¹⁸ Department of Biomedical Engineering, Johns Hopkins School of Medicine and Whiting School of Engineering, Baltimore, MD, USA. [email protected].
¹⁹ Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. [email protected].

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 .

Publication types

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

MeSH terms

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

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding