piRSNP: A Database of piRNA- related SNPs and their Effects on Cancerrelated piRNA Functions-Reference-Cited by-同舟云学术

piRSNP: A Database of piRNA- related SNPs and their Effects on Cancerrelated piRNA Functions

Published:2023-07 Issue:6 Volume:18 Page:509-516
ISSN:1574-8936
Container-title:Current Bioinformatics
language:en
Short-container-title:CBIO

Author:

Liu Yajun¹^ORCID,Li Aimin¹,Zhu Yingda¹,Pang Xinchao¹,Hei Xinhong¹,Xie Guo²,Wu Fang-Xiang³

Affiliation:

1. Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China

2. Shaanxi Key Laboratory of Complex System Control and Intelligent Information Processing, School of Automation and Information Engineering, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China

3. Division of Biomedical Engineering, Department of Mechanical Engineering, Department of Computer Science, University of Saskatchewan, SK, S7N 5A9, Canada

Abstract

Backgroud: PIWI-interacting RNAs (piRNAs) are a kind of small non-coding RNAs which interact with PIWI proteins and play a vital role in safeguarding genome. Single nucleotide polymorphisms (SNPs) are widely distributed variations which are associated with diseases and have rich information. Up to now, various studies have proved that SNPs on piRNA were related to diseases. Objective: In order to create a comprehensive source about piRNA-related SNPs, we developed a publicly available online database piRSNP. Methods: We systematically identified SNPs on human and mouse piRNAs. piRSNP contains 42,967,522 SNPs on 10,773,081 human piRNAs and 29,262,185 SNPs on 16,957,706 mouse piRNAs. Results: 7,446 SNPs on 519 cancer-related piRNAs and their flanks are investigated. Impacts of 2,512 variations of cancer-related piRNAs on piRNA-mRNA interactions are analyzed. Conclusion: All these useful data and piRNA expression profiles of 12 cancer types in both tumor and pericarcinomatous tissues are compiled into piRSNP. piRSNP characterizes human and mouse piRNArelated SNPs comprehensively and could be beneficial for researchers to investigate subsequent piRNA functions. Database URL is http://www.ibiomedical.net/piRSNP/.

Funder

National Natural Science Foundation of China

Natural Science Basic Research Program of Shaanxi Province of China

China Postdoctoral Science Foundation

Publisher

Bentham Science Publishers Ltd.

Subject

Computational Mathematics,Genetics,Molecular Biology,Biochemistry

Reference38 articles.

1. Kim V.N.; Small RNAs just got bigger: Piwi-interacting RNAs (piRNAs) in mammalian testes. Genes Dev 2006,20(15),1993-1997

2. Morceau F.; Chateauvieux S.; Gaigneaux A.; Dicato M.; Diederich M.; Long and short non-coding RNAs as regulators of hematopoietic differentiation. Int J Mol Sci 2013,14(7),14744-14770

3. Grivna S.T.; Beyret E.; Wang Z.; Lin H.; A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 2006,20(13),1709-1714

4. Yan Z.; Hu H.Y.; Jiang X.; Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Res 2011,39(15),6596-6607

5. Martinez V.D.; Vucic E.A.; Thu K.L.; Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology. Sci Rep 2015,5(1),10423

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