Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data

• DOI: 10.3389/fgene.2021.722981
• Publication Date: 2021-08-16T07:19:41Z
• Authors: Jing Li; Urminder Singh; Zebulun Arendsee; Eve Syrkin Wurtele
• Keywords: ORFS; RNA-Seq

The “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression 6,692 genes and 29,354 unannotated open reading frames (ORFs) in Saccharomyces cerevisiae genome across diverse environmental, genetic developmental conditions (3,457 RNA-Seq samples). Over 30% highly ORFs have translation evidence. Phylostratigraphic analysis infers most these would encode species-specific proteins (“orphan-ORFs”); hundreds mean comparable to These data reveal likely protein-coding partitioned a co-expression matrix by Markov Chain Clustering; resultant clusters contain 2,468 orphan-ORFs. provide aggregated yeast with extensive metadata project MetaOmGraph (MOG), tool designed for interactive visualization. This approach enables reuse public exploratory discovery, providing rich context experimentalists make novel, experimentally testable hypotheses about candidate