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

Mihaela Pertea; Alaina Shumate; Geo Pertea; Ales Varabyou; Florian P Breitwieser; Yu-Chi Chang; Anil K Madugundu; Akhilesh Pandey; Steven L Salzberg

doi:10.1186/s13059-018-1590-2

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

Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2.

Authors

Mihaela Pertea^{1

2}, Alaina Shumate^{1

3}, Geo Pertea¹, Ales Varabyou^{1

2}, Florian P Breitwieser¹, Yu-Chi Chang², Anil K Madugundu^{4

5

6

7}, Akhilesh Pandey^{4

8

7}, Steven L Salzberg^{9

10

11

12}

Affiliations

¹ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
² Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
³ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
⁴ McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
⁵ Institute of Bioinformatics, International Technology Park, Bangalore, India.
⁶ Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India.
⁷ Present address: Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
⁸ Departments of Biological Chemistry, Pathology, Neurology, and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
⁹ Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. salzberg@jhu.edu.
¹⁰ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
¹¹ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.
¹² Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. salzberg@jhu.edu.

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 .

Keywords: GTEx; Human gene count; RNA sequencing; Transcriptome; Transcriptome assembly.

Publication types

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

MeSH terms

Amino Acid Sequence
Animals
Databases, Genetic*
Female
Humans
Introns
Male
Sequence Analysis, RNA*
Transcription, Genetic*

Abstract

Publication types

MeSH terms

Grants and funding