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Nucleic Acids Res. 2015 Jan;43(Database issue):D862-7. doi: 10.1093/nar/gku1156. Epub 2014 Nov 14.

YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.

Author information

1
Research Center for Tumor Medical Science, China Medical University, Taichung 40402, Taiwan.
2
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
3
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
4
Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
5
VGH-YM Genomic Research Center, National Yang-Ming University, Taipei 11221, Taiwan.
6
Institute of Clinical Medicine, Medical College, National Yang-Ming University, Taipei 11221, Taiwan Department of Radiation Oncology, Taichung Veterans' General Hospital, Taichung 40705, Taiwan.
7
Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defence Medical Center, Taipei 11490, Taiwan.
8
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.
9
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.

Abstract

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.

PMID:
25398902
PMCID:
PMC4383957
DOI:
10.1093/nar/gku1156
[Indexed for MEDLINE]
Free PMC Article

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