ArticleBMC genomics2018
Comprehensive analysis of coding-lncRNA gene co-expression network uncovers conserved functional lncRNAs in zebrafish.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Frontiers in genetics · 2023Article
- Changes in the Mucosa-Associated Microbiome and Transcriptome across Gut Segments Are Associated with Obesity in a Metabolic Syndrome Porcine Model.Microbiology spectrum · 2022Article
- Systematic identification and characterization of long noncoding RNAs (lncRNAs) during Aedes albopictus development.PLoS neglected tropical diseases · 2022Article
- GCEN: An Easy-to-Use Toolkit for Gene Co-Expression Network Analysis and lncRNAs Annotation.Current issues in molecular biology · 2022Article
- Long Noncoding RNA MIR2187HG Suppresses TBK1-Mediated Antiviral Signaling by Deriving miR-2187-3p in Teleost Fish.Journal of virology · 2022Article
- Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants.BMC genomics · 2021Article
- FGGA-lnc: automatic gene ontology annotation of lncRNA sequences based on secondary structures.Interface focus · 2021Article
- The Use of Zebrafish Xenotransplant Assays to Analyze the Role of lncRNAs in Breast Cancer.Frontiers in oncology · 2021Review
- The physiological function of long-noncoding RNAs.Non-coding RNA research · 2020Review
- Potential Involvement of lncRNAs in the Modulation of the Transcriptome Response to Nodavirus Challenge in European Sea Bass (Biology · 2020Article
- Zebrafish models of sarcopenia.Disease models & mechanisms · 2020Review
- Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression.Functional & integrative genomics · 2020Article
- Long non-coding RNA small nucleolar RNA host gene 7 is upregulated and promotes cell proliferation in thyroid cancer.Oncology letters · 2019Article
- Comparative modulation of lncRNAs in wild-type and rag1-heterozygous mutant zebrafish exposed to immune challenge with spring viraemia of carp virus (SVCV).Scientific reports · 2019Article
- Comprehensive analysis of differentially expressed long non-coding RNAs in non-small cell lung cancer.Oncology letters · 2019Article
- A long noncoding RNA cluster-based genomic locus maintains proper development and visual function.Nucleic acids research · 2019Article
- Biological Network Approach for the Identification of Regulatory Long Non-Coding RNAs Associated With Metabolic Efficiency in Cattle.Frontiers in genetics · 2019Article
- Article
- ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA.Database : the journal of biological databases and curation · 2018Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundZebrafish is a full-developed model system for studying development processes and human disease. Recent studies of deep sequencing had discovered a large number of long non-coding RNAs (lncRNAs) in zebrafish. However, only few of them had been functionally characterized. Therefore, how to take advantage of the mature zebrafish system to deeply investigate the lncRNAs' function and conservation is really intriguing.
resultsWe systematically collected and analyzed a series of zebrafish RNA-seq data, then combined them with resources from known database and literatures. As a result, we obtained by far the most complete dataset of zebrafish lncRNAs, containing 13,604 lncRNA genes (21,128 transcripts) in total. Based on that, a co-expression network upon zebrafish coding and lncRNA genes was constructed and analyzed, and used to predict the Gene Ontology (GO) and the KEGG annotation of lncRNA. Meanwhile, we made a conservation analysis on zebrafish lncRNA, identifying 1828 conserved zebrafish lncRNA genes (1890 transcripts) that have their putative mammalian orthologs. We also found that zebrafish lncRNAs play important roles in regulation of the development and function of nervous system; these conserved lncRNAs present a significant sequential and functional conservation, with their mammalian counterparts.
conclusionsBy integrative data analysis and construction of coding-lncRNA gene co-expression network, we gained the most comprehensive dataset of zebrafish lncRNAs up to present, as well as their systematic annotations and comprehensive analyses on function and conservation. Our study provides a reliable zebrafish-based platform to deeply explore lncRNA function and mechanism, as well as the lncRNA commonality between zebrafish and human.
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