SNMDA: A novel method for predicting microRNA-disease associations based on sparse neighbourhood

Journal of Cellular and Molecular Medicine
Yu QuJiawei Luo

Abstract

miRNAs are a class of small noncoding RNAs that are associated with a variety of complex biological processes. Increasing studies have shown that miRNAs have close relationships with many human diseases. The prediction of the associations between miRNAs and diseases has thus become a hot topic. Although traditional experimental methods are reliable, they could only identify a limited number of associations as they are time-consuming and expensive. Consequently, great efforts have been made to effectively predict reliable disease-related miRNAs based on computational methods. In this study, we present a novel approach to predict the potential microRNA-disease associations based on sparse neighbourhood. Specifically, our method takes advantage of the sparsity of the miRNA-disease association network and integrates the sparse information into the current similarity matrices for both miRNAs and diseases. To demonstrate the utility of our method, we applied global LOOCV, local LOOCV and five-fold cross-validation to evaluate our method, respectively. The corresponding AUCs are 0.936, 0.882 and 0.934. Three types of case studies on five common diseases further confirm the performance of our method in predicting unknown miRNA-disease ...Continue Reading

References

Sep 17, 2004·Nature·Victor Ambros
Nov 4, 2004·Trends in Genetics : TIG·Peizhang XuBruce A Hay
Aug 16, 2005·Current Opinion in Genetics & Development·Eric A Miska
Aug 17, 2005·Cancer Research·Marilena V IorioCarlo M Croce
Mar 15, 2006·Cancer Cell·Nozomu YanaiharaCurtis C Harris
Aug 28, 2007·Methods in Enzymology·J Michael ThomsonScott M Hammond
Dec 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Xu-Bao ShiRalph W deVere White
Mar 29, 2008·American Journal of Human Genetics·Sebastian KöhlerPeter N Robinson
Apr 30, 2010·The New England Journal of Medicine·Manuel Hidalgo
Jun 11, 2010·BMC Systems Biology·Qinghua JiangYadong Wang
Dec 22, 2010·BMC Genomics·Zhen YangHaitao Zhao
Aug 10, 2012·Molecular BioSystems·Xing ChenGui-Ying Yan
Sep 22, 2012·Asian Pacific Journal of Cancer Prevention : APJCP·Dong-Fu LiuYun-Xiang Liu
Sep 25, 2012·Nature·UNKNOWN Cancer Genome Atlas Network
Jan 12, 2013·Molecular Biology Reports·Samira Mohammadi-YeganehMorteza Karimipoor
May 2, 2013·British Journal of Cancer·A Sita-LumsdenC L Bevan
Jan 15, 2014·International Journal of Data Mining and Bioinformatics·Qinghua JiangYadong Wang
Jun 18, 2014·Asian Pacific Journal of Cancer Prevention : APJCP·Ayla Valinezhad OrangMohammad Hossein Somi
Jul 1, 2014·Scientific Reports·Xing Chen, Gui-Ying Yan
Aug 15, 2015·BioMed Research International·Quan ZouYing Ju
Aug 25, 2015·Journal of Cheminformatics·Abhik SealDavid J Wild
Feb 18, 2016·Scientific Reports·Xing ChenQionghai Dai
Apr 15, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yuansheng LiuQuan Zou
Jul 9, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Wei LanYi Pan
Aug 26, 2016·Archives of Toxicology·Klara Piletič, Tanja Kunej
Sep 1, 2017·Journal of Cellular and Molecular Medicine·Xing ChenZheng-Wei Li
Dec 1, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Wen ZhangDingfang Li
Dec 23, 2017·Journal of Cellular and Molecular Medicine·Xing ChenGui-Ying Yan
Mar 14, 2018·Journal of Cellular and Molecular Medicine·Xing ChenLi Huang
Jul 12, 2018·IEEE Transactions on Neural Networks and Learning Systems·Lei ZhuHeng Tao Shen

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Software Mentioned

NDAMDA
EBMMDA
HGIMDA
Mesh
MKRMDA
PBMDA
PhenomiR
EGBMMDA
HMDD
l1

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