title: CircNet: a database of circular RNAs derived from transcriptome sequencing data.
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.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan.
authors.forename: Yu-Chen
authors.initials: YC
authors.lastname: Liu
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan.
authors.forename: Jian-Rong
authors.initials: JR
authors.lastname: Li
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan.
authors.forename: Chuan-Hu
authors.initials: CH
authors.lastname: Sun
authors.affiliation: Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766, USA.
authors.forename: Erik
authors.initials: E
authors.lastname: Andrews
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan.
authors.forename: Rou-Fang
authors.initials: RF
authors.lastname: Chao
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan.
authors.forename: Feng-Mao
authors.initials: FM
authors.lastname: Lin
authors.affiliation: 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.
authors.forename: Shun-Long
authors.initials: SL
authors.lastname: Weng
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, Taiwan.
authors.forename: Sheng-Da
authors.initials: SD
authors.lastname: Hsu
authors.affiliation: Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Chieh-Chen
authors.initials: CC
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan jimliu@nchu.edu.tw.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
mesh_terms: D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D000079962:RNA, Circular; D017423:Sequence Analysis, RNA
chemical_list: D000079962:RNA, Circular; D012313:RNA