PCsRNAdb - Database issue - a comprehensive resource of small noncoding RNAs across cancers

Sep 22, 2026

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Small noncoding RNAs (sncRNAs) include miRNAs, piRNAs, tRNA-derived fragments (tDRs), rRNA-derived fragments (rRFs), and other small RNAs, and they act as key regulatory elements in many biological processes and diseases. While miRNAs are well established, knowledge about non-miRNA sncRNAs in oncology remains limited. PCsRNAdb addresses this gap by integrating 190 GEO/SRA datasets covering 11,114 samples across 19 cancer types, delivering sequence, length, abundance, target genes, and multiple advanced analyses including differential expression, survival, expression profiling, and network regulation.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages11

Reading Time28 min

AccessFree to download

Abstract

Database overview

Dataset collection and scope

Data and analysis functionalities

Nucleic Acids Research, 2026, 54, D1545–D1555 [https://doi.org/10.1093/nar/gkaf992](https://doi.org/10.1093/nar/gkaf992) Advance access publication date: 8 October 2025 Database issue PCsRNAdb: a comprehensive resource of small noncoding RNAs across cancers Rende Huang1 ,2 ,3 ,4 ,†, Jiang Li5 ,†, Qi Cao2 , 6 ,†, Lixia Wang7 ,†, Zhixiong Shao2 , 6 , Haochun Yang2 , 6 , Xinlei Zhang8 , Chuanlai Yang7 , Xiangya Kong8 , Qiuyue Gu8 , Jianmin Wu6 ,9 , Tsan-Yu Chiu6 , Penghu Lian 10 , *, Kui Wu2 , 11 , *, Feng Gao 1 ,3 ,4 , *, Zhongxu Zhu 2 , 6 , * 1 Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China 2Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310018, China 3 Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China 4 Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China 5 Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China 6 Biomics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310018, China 7 Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu 215006, China 8 Beijing Cloudna Technology Company, Limited, Beijing 100029, China 9 Key Laboratory of Laboratory Medicine, Ministry of Education, Institute of Genomic Medicine, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Zhejiang 325035, China 10 Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China 11 Jiangxi Provincial Key Laboratory of Organ Development and Epigenetics, School of Basic Medicine, Jinggangshan University, Ji’an 343009, China * To whom correspondence should be addressed. Email: [zhuzhongxu@him.cas.cn](zhuzhongxu@him.cas.cn) Correspondence may also be addressed to Feng Gao. Email: [gaof57@mail.sysu.edu.cn](gaof57@mail.sysu.edu.cn) Correspondence may also be addressed to [Kui Wu. Email: wukui@him.cas.cn](Kui Wu. Email: wukui@him.cas.cn) Correspondence may also be addressed to Penghu Lian. Email: [lianpenghu@126.com](lianpenghu@126.com) †The first four authors should be regarded as Joint First Authors. Abstract Small noncoding RNAs (sncRNAs) constitute a diverse class of endogenous transcripts, including miRNAs, piRNAs, tRNA-derived fragments (tDRs), rRNA-derived fragments (rRFs), and other small RNAs. They have been identified as pivotal regulatory elements in a wide array of biological processes and diseases. Among these, miRNA is the most extensively studied and confirmed as a key regulatory and diagnostic biomarker in tumorigenesis and development. However, the current understanding of sncRNAs other than miRNA remains limited, particularly in the field of oncology. To this end, we collected 190 datasets from GEO/SRA database, encompassing 11 114 samples across 19 cancer types, and built a user-friendly database, the Pan-Cancer Small Non-Coding RNA Database (PCsRNAdb, [http://pcsrnadb.cloudna.cn/\#/Home](http://pcsrnadb.cloudna.cn/#/Home)), which is developed to provide abundant resources of sncRNAs specifically designed to investigate the association between sncRNAs and cancers. PCsRNAdb comprehensively provides basic information such as the sequence, length, abundance, and target genes of sncRNAs, and further offers four advanced functionalities, including differential expression analysis, survival analysis, expression profiling analysis, and network regulatory analysis. We anticipate that such platform offers invaluable resources and effective analytical tools for researchers in related fields and is expected to facilitate cancer-related research in this domain. Graphical abstract Received: July 22, 20

FAQs

What types of small noncoding RNAs does PCsRNAdb support?

PCsRNAdb covers sncRNAs including miRNAs, piRNAs, tRNA-derived fragments (tDRs), rRNA-derived fragments (rRFs), and other small RNAs.

How many datasets and samples are included in PCsRNAdb?

PCsRNAdb collects 190 datasets from GEO/SRA encompassing 11,114 samples across 19 cancer types.

Which advanced functions are provided by the PCsRNAdb database?

PCsRNAdb offers differential expression analysis, survival analysis, expression profiling analysis, and network regulatory analysis.

Sep 22, 2026

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