ZFIN ID: ZDB-PUB-150613-3
zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs
Dhiman, H., Kapoor, S., Sivadas, A., Sivasubbu, S., Scaria, V.
Date: 2015
Source: PLoS One   10: e0129997 (Journal)
Registered Authors: Sivasubbu, Sridhar
Keywords: none
MeSH Terms:
  • Animals
  • Databases, Nucleic Acid*
  • Genomics/methods
  • High-Throughput Nucleotide Sequencing/methods
  • Humans
  • Internet*
  • Molecular Sequence Annotation
  • Promoter Regions, Genetic/genetics
  • RNA, Long Noncoding/genetics*
  • Sequence Analysis, RNA/methods*
  • Software*
  • Transcriptome
  • Zebrafish/genetics*
PubMed: 26065909 Full text @ PLoS One
Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncRNAs. In the present report, we created a catalog of lncRNAs in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncRNA transcripts in zebrafish. The lncRNAs were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. Analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincRNAs. We created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. The resource also hosts a genome browser where the datasets could be browsed in the genome context. To the best of our knowledge, this is the first comprehensive resource providing a unified catalog of lncRNAs in zebrafish. The resource is freely available at URL: http://genome.igib.res.in/zflncRNApedia.