Format

Send to

Choose Destination
Nucleic Acids Res. 2017 Jan 4;45(D1):D925-D931. doi: 10.1093/nar/gkw1084. Epub 2016 Nov 29.

YM500v3: a database for small RNA sequencing in human cancer research.

Author information

1
Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.
2
Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu City 30071, Taiwan.
3
Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan.
4
Research Center for Tumour Medical Science, China Medical University, Taichung, 40402, Taiwan.
5
Department of Genome Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
6
Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
7
Graduate Institute of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan cwc0702@gmail.com.

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.

PMID:
27899625
PMCID:
PMC5210564
DOI:
10.1093/nar/gkw1084
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center