YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
Research Center for Tumor Medical Science, China Medical University, Taichung 40402, Taiwan.
Wei-Chung
WC
Cheng
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
I-Fang
IF
Chung
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
Cheng-Fong
CF
Tsai
Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Tse-Shun
TS
Huang
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
Chen-Yang
CY
Chen
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
Shao-Chuan
SC
Wang
VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
Ting-Yu
TY
Chang
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
Hsing-Jen
HJ
Sun
Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Department of Radiation Oncology, Taichung Veterans' General Hospital, Taichung 40705, Taiwan.
Jeffrey Yung-Chuan
JY
Chao
Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Center, Taipei 11490, Taiwan.
Cheng-Chung
CC
Cheng
Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Biomedical Science, Academia Sinica, Taipei 11529, Taiwan Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei 11221, Taiwan.
Cheng-Wen
CW
Wu
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 11221, Taiwan Department of Education and Research, Taipei City Hospital, Taipei 10341, Taiwan hwwang@ym.edu.tw.
Hsei-Wei
HW
Wang
D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000737:chemistry* / Q000378:metabolism*; D009369:Neoplasms / Q000235:genetics*; D017423:Sequence Analysis, RNA
D035683:MicroRNAs