title: YM500v3: a database for small RNA sequencing in human cancer research.
abstract: We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, 'Survival' and 'Cancer', in this updated version. The 'Survival' section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The 'Cancer' section provides the results of differential expression analyses, miRNA-gene interactions and cancer miRNA-related pathways. In the 'Expression' section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
authors.forename: I-Fang
authors.initials: IF
authors.lastname: Chung
authors.affiliation: Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan.
authors.forename: Shing-Jyh
authors.initials: SJ
authors.lastname: Chang
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
authors.forename: Chen-Yang
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.|Research Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan.
authors.forename: Shu-Hsuan
authors.initials: SH
authors.lastname: Liu
authors.affiliation: Department of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.|Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors.forename: Chia-Yang
authors.initials: CY
authors.lastname: Li
authors.affiliation: Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan.
authors.forename: Chia-Hao
authors.initials: CH
authors.lastname: Chan
authors.affiliation: Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan.
authors.forename: Chuan-Chi
authors.initials: CC
authors.lastname: Shih
authors.affiliation: Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan cwc0702@gmail.com.|Research Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan.
authors.forename: Wei-Chung
authors.initials: WC
authors.lastname: Cheng
mesh_terms: D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D009369:Neoplasms / Q000235:genetics* / Q000401:mortality; D011379:Prognosis; D058727:RNA, Small Untranslated / Q000737:chemistry*; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D058727:RNA, Small Untranslated