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Current Bioinformatics

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ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

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General Research Article

A Novel Model for Predicting LncRNA-disease Associations based on the LncRNA-MiRNA-Disease Interactive Network

Author(s): Lei Wang, Zhanwei Xuan*, Shunxian Zhou, Linai Kuang and Tingrui Pei

Volume 14, Issue 3, 2019

Page: [269 - 278] Pages: 10

DOI: 10.2174/1574893613666180703105258

Price: $65

Abstract

Background: Accumulating experimental studies have manifested that long-non-coding RNAs (lncRNAs) play an important part in various biological process. It has been shown that their alterations and dysregulations are closely related to many critical complex diseases.

Objective: It is of great importance to develop effective computational models for predicting potential lncRNA-disease associations.

Method: Based on the hypothesis that there would be potential associations between a lncRNA and a disease if both of them have associations with the same group of microRNAs, and similar diseases tend to be in close association with functionally similar lncRNAs. A novel method for calculating similarities of both lncRNAs and diseases is proposed, and then a novel prediction model LDLMD for inferring potential lncRNA-disease associations is proposed.

Results: LDLMD can achieve an AUC of 0.8925 in the Leave-One-Out Cross Validation (LOOCV), which demonstrated that the newly proposed model LDLMD significantly outperforms previous state-of-the-art methods and could be a great addition to the biomedical research field.

Conclusion: Here, we present a new method for predicting lncRNA-disease associations, moreover, the method of our present decrease the time and cost of biological experiments.

Keywords: Similarity， computing model， prediction, lncRNA-disease associations, LncRNA-MiRNA-disease interactive network.

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[1]
Batista P, Chang H. Long Noncoding RNAs: Cellular Address Codes in Development and Disease. Cell 2013; 152(6): 1298-307.
[2]
Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011; 43(6): 904-14.
[3]
Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136(4): 629-41.
[4]
Zheng J, Peng H, Wang L. Similarities/Dissimilarities Analysis of Protein Sequences Based on Recurrence Quantification Analysis. Curr Bioinform 2015; 10(1): 112-9.
[5]
Uchida S, Dimmeler S. Long noncoding RNAs in cardiovascular diseases. Circ Res 2015; 116(4): 737-50.
[6]
Johnson R. Long non-coding RNAs in Huntington’s disease neurodegeneration. Neurobiol Dis 2012; 46(2): 245-54.
[7]
Pasmant E, Sabbagh A, Vidaud M, Bièche I. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J 2011; 25(2): 444-8.
[8]
Quan Z, Chen CY, Yedavalli VSRK, Kuan-Teh J. NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression. MBio 2013; 4(1): e00596-12.
[9]
Lau SK, Ming ST, Barsyte-Lovejoy D, et al. The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Res 2006; 66(10): 5330-7.
[10]
Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464(7291): 1071-6.
[11]
Calin GA, Liu CG, Ferracin M, et al. Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 2007; 12(3): 215-29.
[12]
Panzitt K, Tschernatsch MM, Guelly C, et al. Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 2007; 132(1): 330-42.
[13]
de Kok JB, Verhaegh GW, Roelofs RW, et al. DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res 2002; 62(9): 2695-8.
[14]
Széll M, Bata-Csörgo Z, Kemény L. The enigmatic world of mRNA-like ncRNAs: their role in human evolution and in human diseases. Semin Cancer Biol 2008; 18(2): 141-8.
[15]
Zhang X, Zhou Y, Mehta KR, et al. A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. J Clin Endocrinol Metab 2003; 88(11): 5119-26.
[16]
Maass PG, Luft FC, Bähring S. Long non-coding RNA in health and disease. J Mol Med 2014; 92(4): 337-46.
[17]
Kogo R, Shimamura T, Mimori K, et al. Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers. Cancer Res 2011; 71(20): 6320-6.
[18]
Li G, Zhang H, Wan X, et al. Long noncoding RNA plays a key role in metastasis and prognosis of hepatocellular carcinoma. BioMed Res Int 2014; 2014(5147): 780521.
[19]
Liu X, Sun M, Nie F, et al. Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer. Mol Cancer 2014; 13(1): 92.
[20]
Hrdlickova B, de Almeida RC, Borek Z, Withoff S. Genetic variation in the non-coding genome: Involvement of micro-RNAs and long non-coding RNAs in disease. Biochim Biophys Acta 2014; 1842(10): 1910-22.
[21]
Geng C, Wang Z, Wang D, et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 2013; 41: 983-6.
[22]
Lan W, Li M, Zhao K, et al. LDAP: a web server for lncRNA-disease association prediction. Bioinformatics 2017; 33(3): 458-60.
[23]
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011; 39: 146-51.
[24]
Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458(7235): 223-7.
[25]
Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer 2011; 10(1): 38.
[26]
Geisler S, Coller J. RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 2013; 14(11): 699-712.
[27]
Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464(7291): 1071-6.
[28]
Chung S, Nakagawa H, Uemura M, et al. Association of a novel long non-coding RNA in 8q24 with prostate cancer susceptibility. Cancer Sci 2011; 102(1): 245-52.
[29]
Mohanty V, Gökmenpolar Y, Badve S, Janga SC. Role of lncRNAs in health and disease-size and shape matter. Brief Funct Genomics 2015; 14(2): 115-29.
[30]
Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 2015; 5: 13186.
[31]
Chen X, Yan GY. Novel human lncRNA-disease association inference based on lncRNA expression profiles. Bioinformatics 2013; 29(20): 2617-24.
[32]
Sun J, Shi H, Wang Z, et al. Inferring novel lncRNA–disease associations based on a random walk model of a lncRNA functional similarity network. Mol Biosyst 2014; 10(8): 2074-81.
[33]
Li J, Gao C, Wang Y, et al. A bioinformatics method for predicting long noncoding RNAs associated with vascular disease. Sci China Life Sci 2014; 57(8): 852-7.
[34]
Yang X, Gao L, Guo X, et al. A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases. PLoS One 2014; 9(1): e87797.
[35]
Zhao T, Xu J, Liu L, et al. Identification of cancer-related lncRNAs through integrating genome, regulome and transcriptome features. Mol Biosyst 2015; 11(1): 126-36.
[36]
Zhou M, Wang X, Li J, et al. Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network. Mol Biosyst 2015; 11(3): 760.
[37]
Zhang L, Deng Q, Su Y, Hu Y. A Box-Covering-Based Routing Algorithm for Large-Scale SDNs. IEEE Access 2017. 5(99): 4048- 56.
[38]
Chen X, Huang YA, You ZH, Yan GY, Wang XS. A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases. Bioinformatics 2016; 33(5): 733-9.
[39]
Wang L, Ping P, Kuang L, Ye S, Buland Lqbal FM, Pei T. A Novel Approach based on Bipartite Network to Predict Human Microbe-Disease Associations. Curr Bioinform 2018; 14: 269-78.

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