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

Research output: Contribution to journalArticle

34 Scopus citations

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.

Original languageEnglish (US)
Article number208
JournalGenome biology
Volume19
Issue number1
DOIs
StatePublished - Nov 28 2018

Keywords

  • GTEx
  • Human gene count
  • RNA sequencing
  • Transcriptome
  • Transcriptome assembly

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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    Pertea, M., Shumate, A., Pertea, G., Varabyou, A., Breitwieser, F. P., Chang, Y. C., Madugundu, A. K., Pandey, A., & Salzberg, S. L. (2018). CHESS: A new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise. Genome biology, 19(1), [208]. https://doi.org/10.1186/s13059-018-1590-2