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

doi:10.1093/nar/gkw1084

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

Institute of Biomedical Informatics

Research output: Contribution to journal › Article › peer-review

44 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 language	English
Pages (from-to)	D925-D931
Journal	Nucleic acids research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw1084
State	Published - 1 Jan 2017

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title = "YM500v3: A database for small RNA sequencing in human cancer research",

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.",

author = "Chung, {I. Fang} and Chang, {Shing Jyh} and Chen, {Chen Yang} and Liu, {Shu Hsuan} and Li, {Chia Yang} and Chan, {Chia Hao} and Shih, {Chuan Chi} and Cheng, {Wei Chung}",

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AU - Chung, I. Fang

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AU - Liu, Shu Hsuan

AU - Li, Chia Yang

AU - Chan, Chia Hao

AU - Shih, Chuan Chi

AU - Cheng, Wei Chung

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

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