YM500v3: A database for small RNA sequencing in human cancer research

I. Fang Chung, Shing Jyh Chang, Chen Yang Chen, Shu Hsuan Liu, Chia Yang Li, Chia Hao Chan, Chuan Chi Shih, Wei Chung Cheng*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

37 Scopus citations

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), tRNAderived 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.

Original languageEnglish
Pages (from-to)D925-D931
JournalNucleic acids research
Volume45
Issue numberD1
DOIs
StatePublished - 1 Jan 2017

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