title: zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs.
abstract: 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.
authors.affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India.
authors.forename: Heena
authors.initials: H
authors.lastname: Dhiman
authors.affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi, 110001, India.
authors.forename: Shruti
authors.initials: S
authors.lastname: Kapoor
authors.affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India.
authors.forename: Ambily
authors.initials: A
authors.lastname: Sivadas
authors.affiliation: Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Sivasubbu
authors.affiliation: GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi, 110001, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics*
chemical_list: D062085:RNA, Long Noncoding