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

Wei Chung Cheng, I. Fang Chung, Cheng Fong Tsai, Tse Shun Huang, Chen Yang Chen, Shao Chuan Wang, Ting Yu Chang, Hsing Jen Sun, Jeffrey Yung Chuan Chao, Cheng Chung Cheng, Cheng-Wen Wu, Hsei Wei Wang*

*Corresponding author for this work

Research output: Contribution to journalArticle

35 Scopus citations

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.

Original languageEnglish
Pages (from-to)D862-D867
JournalNucleic acids research
Volume43
Issue numberD1
DOIs
StatePublished - 15 Jan 2015

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    Cheng, W. C., Chung, I. F., Tsai, C. F., Huang, T. S., Chen, C. Y., Wang, S. C., Chang, T. Y., Sun, H. J., Chao, J. Y. C., Cheng, C. C., Wu, C-W., & Wang, H. W. (2015). YM500v2: A small RNA sequencing (smRNA-seq) database for human cancer miRNome research. Nucleic acids research, 43(D1), D862-D867. https://doi.org/10.1093/nar/gku1156