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Nucleic Acids Res. 2016 Jan 4;44(D1):D209-15. doi: 10.1093/nar/gkv940. Epub 2015 Oct 7.

CircNet: a database of circular RNAs derived from transcriptome sequencing data.

Author information

1
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan.
2
Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan.
3
Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA.
4
Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan Mackay Medicine, Nursing and Management College, Taipei, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, Taiwan.
5
Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
6
Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA.
7
Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan jimliu@nchu.edu.tw.
8
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 300, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan bryan@mail.nctu.edu.tw.

Abstract

Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database (http://circnet.mbc.nctu.edu.tw/) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA-miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.

PMID:
26450965
PMCID:
PMC4702939
DOI:
10.1093/nar/gkv940
[Indexed for MEDLINE]
Free PMC Article

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