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Volumn 7, Issue 36, 2016, Pages 57919-57931

IRWRLDA: Improved random walk with restart for lncRNA-disease association prediction

Author keywords

Cancer; Disease; lncRNAs; Random walk with restart

Indexed keywords

LONG UNTRANSLATED RNA;

EID: 84988349835     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.11141     Document Type: Article
Times cited : (201)

References (79)
  • 1
    • 0000818999 scopus 로고
    • General Nature of the Genetic Code for Proteins
    • Crick F, Barnett L, Brenner S, Watts-Tobin R. General Nature of the Genetic Code for Proteins. Nature. 1961; 192:1227-1232.
    • (1961) Nature. , vol.192 , pp. 1227-1232
    • Crick, F.1    Barnett, L.2    Brenner, S.3    Watts-Tobin, R.4
  • 2
    • 33847359927 scopus 로고    scopus 로고
    • Establishing the triplet nature of the genetic code
    • Yanofsky C. Establishing the triplet nature of the genetic code. Cell. 2007; 128:815-818.
    • (2007) Cell. , vol.128 , pp. 815-818
    • Yanofsky, C.1
  • 4
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell. 2009; 136:629-641.
    • (2009) Cell. , vol.136 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 9
    • 24644505259 scopus 로고    scopus 로고
    • Fewer genes, more noncoding RNA
    • Claverie JM. Fewer genes, more noncoding RNA. Science. 2005; 309:1529-1530.
    • (2005) Science. , vol.309 , pp. 1529-1530
    • Claverie, J.M.1
  • 10
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008; 322:1845-1848.
    • (2008) Science. , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 13
    • 33847698971 scopus 로고    scopus 로고
    • The relationship between non_protein_coding DNA and eukaryotic complexity
    • Taft RJ, Pheasant M, Mattick JS. The relationship between non_protein_coding DNA and eukaryotic complexity. Bioessays. 2007; 29:288-299.
    • (2007) Bioessays. , vol.29 , pp. 288-299
    • Taft, R.J.1    Pheasant, M.2    Mattick, J.S.3
  • 14
    • 81355142141 scopus 로고    scopus 로고
    • Non-coding RNAs in human disease
    • Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011; 12:861-874.
    • (2011) Nat Rev Genet. , vol.12 , pp. 861-874
    • Esteller, M.1
  • 15
    • 84875057736 scopus 로고    scopus 로고
    • Long non-coding RNA in cancer
    • Hauptman N, Glavac D. Long non-coding RNA in cancer. Int J Mol Sci. 2013; 14:4655-4669.
    • (2013) Int J Mol Sci. , vol.14 , pp. 4655-4669
    • Hauptman, N.1    Glavac, D.2
  • 16
  • 17
    • 84879969127 scopus 로고    scopus 로고
    • Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins
    • Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 2013; 154:240-251.
    • (2013) Cell. , vol.154 , pp. 240-251
    • Guttman, M.1    Russell, P.2    Ingolia, N.T.3    Weissman, J.S.4    Lander, E.S.5
  • 22
    • 0026489906 scopus 로고
    • The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus
    • Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell. 1992; 71:515-526.
    • (1992) Cell. , vol.71 , pp. 515-526
    • Brockdorff, N.1    Ashworth, A.2    Kay, G.F.3    McCabe, V.M.4    Norris, D.P.5    Cooper, P.J.6    Swift, S.7    Rastan, S.8
  • 24
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011; 25:1915-1927.
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 29
    • 84455206362 scopus 로고    scopus 로고
    • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    • Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell. 2011; 147:1537-1550.
    • (2011) Cell. , vol.147 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 31
    • 84907500489 scopus 로고    scopus 로고
    • LncRNA: a link between RNA and cancer
    • Yang G, Lu X, Yuan L. LncRNA: a link between RNA and cancer. Biochim Biophys Acta. 2014; 1839:1097-1109.
    • (2014) Biochim Biophys Acta. , vol.1839 , pp. 1097-1109
    • Yang, G.1    Lu, X.2    Yuan, L.3
  • 32
    • 84876073407 scopus 로고    scopus 로고
    • Long Noncoding RNAs: Insights from Biological Features and Functions to Diseases
    • Li X, Wu Z, Fu X, Han W. Long Noncoding RNAs: Insights from Biological Features and Functions to Diseases. Med Res Rev. 2012; 33:517-553.
    • (2012) Med Res Rev. , vol.33 , pp. 517-553
    • Li, X.1    Wu, Z.2    Fu, X.3    Han, W.4
  • 38
    • 79955544721 scopus 로고    scopus 로고
    • Functional characterization of the plasmacytoma variant translocation 1 gene (PVT1) in diabetic nephropathy
    • Alvarez ML, DiStefano JK. Functional characterization of the plasmacytoma variant translocation 1 gene (PVT1) in diabetic nephropathy. PLoS One. 2011; 6:e18671.
    • (2011) PLoS One. , vol.6
    • Alvarez, M.L.1    DiStefano, J.K.2
  • 41
    • 84899552234 scopus 로고    scopus 로고
    • Overexpression of lncRNA H19 enhances carcinogenesis and metastasis of gastric cancer
    • Li H, Yu B, Li J, Su L, Yan M, Zhu Z, Liu B. Overexpression of lncRNA H19 enhances carcinogenesis and metastasis of gastric cancer. Oncotarget. 2014; 5:2318-29. doi: 10.18632/ oncotarget.1913.
    • (2014) Oncotarget. , vol.5 , pp. 2318-2329
    • Li, H.1    Yu, B.2    Li, J.3    Su, L.4    Yan, M.5    Zhu, Z.6    Liu, B.7
  • 42
    • 84867900638 scopus 로고    scopus 로고
    • Long noncoding RNAs and cancer: a new frontier of translational research?
    • Spizzo R, Almeida M, Colombatti A, Calin G. Long noncoding RNAs and cancer: a new frontier of translational research? Oncogene. 2012; 31:4577-4587.
    • (2012) Oncogene. , vol.31 , pp. 4577-4587
    • Spizzo, R.1    Almeida, M.2    Colombatti, A.3    Calin, G.4
  • 43
    • 84967109506 scopus 로고    scopus 로고
    • ILNCSIM: improved lncRNA functional similarity calculation model
    • Huang Y, Chen X, You Z, Huang D, Chan K. ILNCSIM: improved lncRNA functional similarity calculation model. Oncotarget. 2016; 7:25902-25914. doi: 10.18632/ oncotarget.8296.
    • (2016) Oncotarget. , vol.7 , pp. 25902-25914
    • Huang, Y.1    Chen, X.2    You, Z.3    Huang, D.4    Chan, K.5
  • 45
    • 85007480726 scopus 로고    scopus 로고
    • Sequencebased prediction of protein-protein interactions using weighted sparse representation model combined with global encoding
    • Huang YA, You ZH, Chen X, Chan K, Luo X. Sequencebased prediction of protein-protein interactions using weighted sparse representation model combined with global encoding. BMC bioinformatics. 2016; 17:184.
    • (2016) BMC bioinformatics. , vol.17 , pp. 184
    • Huang, Y.A.1    You, Z.H.2    Chen, X.3    Chan, K.4    Luo, X.5
  • 47
    • 84941123718 scopus 로고    scopus 로고
    • RBMMMDA: predicting multiple types of diseasemicroRNA associations
    • Chen X, Yan CC, Zhang X, Li Z, Deng L, Zhang Y, Dai Q. RBMMMDA: predicting multiple types of diseasemicroRNA associations. Sci Rep. 2015; 5:13877.
    • (2015) Sci Rep. , vol.5 , pp. 13877
    • Chen, X.1    Yan, C.C.2    Zhang, X.3    Li, Z.4    Deng, L.5    Zhang, Y.6    Dai, Q.7
  • 48
    • 84885644151 scopus 로고    scopus 로고
    • Novel human lncRNA-disease association inference based on lncRNA expression profiles
    • Chen X, Yan GY. Novel human lncRNA-disease association inference based on lncRNA expression profiles. Bioinformatics. 2013; 29:2617-2624.
    • (2013) Bioinformatics. , vol.29 , pp. 2617-2624
    • Chen, X.1    Yan, G.Y.2
  • 49
    • 84939498768 scopus 로고    scopus 로고
    • Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA
    • Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep. 2015; 5:13186.
    • (2015) Sci Rep. , vol.5 , pp. 13186
    • Chen, X.1
  • 50
    • 84903650418 scopus 로고    scopus 로고
    • Semi-supervised learning for potential human microRNA-disease associations inference
    • Chen X, Yan GY. Semi-supervised learning for potential human microRNA-disease associations inference. Sci Rep. 2014; 4:5501.
    • (2014) Sci Rep. , vol.4 , pp. 5501
    • Chen, X.1    Yan, G.Y.2
  • 51
    • 84865295522 scopus 로고    scopus 로고
    • Prediction of Disease-Related Interactions between MicroRNAs and Environmental Factors Based on a Semi-Supervised Classifier
    • Chen X, Liu MX, Cui QH, Yan GY. Prediction of Disease-Related Interactions between MicroRNAs and Environmental Factors Based on a Semi-Supervised Classifier. PloS One. 2012; 7:e43425.
    • (2012) PloS One. , vol.7
    • Chen, X.1    Liu, M.X.2    Cui, Q.H.3    Yan, G.Y.4
  • 52
    • 84931281632 scopus 로고    scopus 로고
    • Constructing lncRNA functional similarity network based on lncRNAdisease associations and disease semantic similarity
    • Chen X, Yan CC, Luo C, Ji W, Zhang Y, Dai Q. Constructing lncRNA functional similarity network based on lncRNAdisease associations and disease semantic similarity. Sci Rep. 2015; 5:11338.
    • (2015) Sci Rep. , vol.5 , pp. 11338
    • Chen, X.1    Yan, C.C.2    Luo, C.3    Ji, W.4    Zhang, Y.5    Dai, Q.6
  • 53
    • 84903751248 scopus 로고    scopus 로고
    • Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network
    • Sun J, Shi H, Wang Z, Zhang C, Liu L, Wang L, He W, Hao D, Liu S, Zhou M. Inferring novel lncRNA-disease associations based on a random walk model of a lncRNA functional similarity network. Mol Biosyst. 2014; 10:2074-2081.
    • (2014) Mol Biosyst. , vol.10 , pp. 2074-2081
    • Sun, J.1    Shi, H.2    Wang, Z.3    Zhang, C.4    Liu, L.5    Wang, L.6    He, W.7    Hao, D.8    Liu, S.9    Zhou, M.10
  • 54
    • 84923347799 scopus 로고    scopus 로고
    • Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network
    • Zhou M, Wang X, Li J, Hao D, Wang Z, Shi H, Han L, Zhou H, Sun J. Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network. Mol Biosyst. 2015; 11:760-769.
    • (2015) Mol Biosyst. , vol.11 , pp. 760-769
    • Zhou, M.1    Wang, X.2    Li, J.3    Hao, D.4    Wang, Z.5    Shi, H.6    Han, L.7    Zhou, H.8    Sun, J.9
  • 55
    • 84900457632 scopus 로고    scopus 로고
    • A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases
    • Yang X, Gao L, Guo X, Shi X, Wu H, Song F, Wang B. A network based method for analysis of lncRNA-disease associations and prediction of lncRNAs implicated in diseases. PLoS One. 2014; 9:e87797.
    • (2014) PLoS One. , vol.9
    • Yang, X.1    Gao, L.2    Guo, X.3    Shi, X.4    Wu, H.5    Song, F.6    Wang, B.7
  • 56
    • 84947272475 scopus 로고    scopus 로고
    • KATZLDA: KATZ measure for the lncRNAdisease association prediction
    • Chen X. KATZLDA: KATZ measure for the lncRNAdisease association prediction. Sci Rep. 2015; 5:16840.
    • (2015) Sci Rep. , vol.5 , pp. 16840
    • Chen, X.1
  • 57
    • 84894258048 scopus 로고    scopus 로고
    • A computational framework to infer human disease-associated long noncoding RNAs
    • Liu MX, Chen X, Chen G, Cui QH, Yan GY. A computational framework to infer human disease-associated long noncoding RNAs. PLoS One. 2014; 9:e84408.
    • (2014) PLoS One. , vol.9
    • Liu, M.X.1    Chen, X.2    Chen, G.3    Cui, Q.H.4    Yan, G.Y.5
  • 58
    • 84905650933 scopus 로고    scopus 로고
    • A bioinformatics method for predicting long noncoding RNAs associated with vascular disease
    • Li J, Gao C, Wang Y, Ma W, Tu J, Wang J, Chen Z, Kong W, Cui Q. A bioinformatics method for predicting long noncoding RNAs associated with vascular disease. Sci China Life Sci. 2014; 57:852-857.
    • (2014) Sci China Life Sci. , vol.57 , pp. 852-857
    • Li, J.1    Gao, C.2    Wang, Y.3    Ma, W.4    Tu, J.5    Wang, J.6    Chen, Z.7    Kong, W.8    Cui, Q.9
  • 59
    • 84865786695 scopus 로고    scopus 로고
    • RWRMDA: predicting novel human microRNA-disease associations
    • Chen X, Liu MX, Yan G. RWRMDA: predicting novel human microRNA-disease associations. Mol Biosyst. 2012; 8:2792-2798.
    • (2012) Mol Biosyst. , vol.8 , pp. 2792-2798
    • Chen, X.1    Liu, M.X.2    Yan, G.3
  • 60
    • 84961325932 scopus 로고    scopus 로고
    • miREFRWR: a novel disease-related microRNAenvironmental factor interactions prediction method
    • Chen X. miREFRWR: a novel disease-related microRNAenvironmental factor interactions prediction method. Mol Biosyst. 2016; 12:624-633.
    • (2016) Mol Biosyst. , vol.12 , pp. 624-633
    • Chen, X.1
  • 61
    • 84862215494 scopus 로고    scopus 로고
    • Drug-target interaction prediction by random walk on the heterogeneous network
    • Chen X, Liu MX, Yan G. Drug-target interaction prediction by random walk on the heterogeneous network. Mol Bio Syst. 2012; 8:1970-1978.
    • (2012) Mol Bio Syst. , vol.8 , pp. 1970-1978
    • Chen, X.1    Liu, M.X.2    Yan, G.3
  • 63
    • 41549139527 scopus 로고    scopus 로고
    • Walking the interactome for prioritization of candidate disease genes
    • Köhler S, Bauer S, Horn D, Robinson PN. Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet. 2008; 82:949-958.
    • (2008) Am J Hum Genet. , vol.82 , pp. 949-958
    • Köhler, S.1    Bauer, S.2    Horn, D.3    Robinson, P.N.4
  • 64
    • 77956047866 scopus 로고    scopus 로고
    • A novel candidate disease genes prioritization method based on module partition and rank fusion
    • Chen X, Yan GY, Liao XP. A novel candidate disease genes prioritization method based on module partition and rank fusion. OMICS. 2010; 14:337-356.
    • (2010) OMICS. , vol.14 , pp. 337-356
    • Chen, X.1    Yan, G.Y.2    Liao, X.P.3
  • 65
    • 84944046390 scopus 로고    scopus 로고
    • Long noncoding RNA expression patterns in lymph node metastasis in colorectal cancer by microarray
    • Rui Q, Xu Z, Yang P, He Z. Long noncoding RNA expression patterns in lymph node metastasis in colorectal cancer by microarray. Biomed Pharmacother. 2015; 75:12-18.
    • (2015) Biomed Pharmacother. , vol.75 , pp. 12-18
    • Rui, Q.1    Xu, Z.2    Yang, P.3    He, Z.4
  • 66
    • 84900824816 scopus 로고    scopus 로고
    • Tissue-based biomarkers predicting outcomes in metastatic colorectal cancer: a review
    • Ung L, Lam AY, Morris D, Chua T. Tissue-based biomarkers predicting outcomes in metastatic colorectal cancer: a review. Clin Transl Oncol. 2014; 16:425-435.
    • (2014) Clin Transl Oncol. , vol.16 , pp. 425-435
    • Ung, L.1    Lam, A.Y.2    Morris, D.3    Chua, T.4
  • 69
    • 84941600969 scopus 로고    scopus 로고
    • Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer
    • Liao Q, He W, Liu J, Cen Y, Luo L, Yu C, Li Y, Chen S, Duan S. Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer. Gene. 2015; 572:259-265.
    • (2015) Gene. , vol.572 , pp. 259-265
    • Liao, Q.1    He, W.2    Liu, J.3    Cen, Y.4    Luo, L.5    Yu, C.6    Li, Y.7    Chen, S.8    Duan, S.9
  • 70
    • 84944453326 scopus 로고    scopus 로고
    • NEAT expression is associated with tumor recurrence and unfavorable prognosis in colorectal cancer
    • Li Y, Chen W, He F, Tan Z, Zheng J, Wang W, Zhao Q, Li J. NEAT expression is associated with tumor recurrence and unfavorable prognosis in colorectal cancer. Oncotarget. 2015; 6:27641-27650. doi: 10.18632/oncotarget.4737.
    • (2015) Oncotarget. , vol.6 , pp. 27641-27650
    • Li, Y.1    Chen, W.2    He, F.3    Tan, Z.4    Zheng, J.5    Wang, W.6    Zhao, Q.7    Li, J.8
  • 75
    • 84919626787 scopus 로고    scopus 로고
    • Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data
    • Wang E, Zaman N, Mcgee S, Milanese JS, Masoudi-Nejad A, O'Connor-McCourt M. Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Semin Cancer Biol. 2015; 30:4-12.
    • (2015) Semin Cancer Biol. , vol.30 , pp. 4-12
    • Wang, E.1    Zaman, N.2    Mcgee, S.3    Milanese, J.S.4    Masoudi-Nejad, A.5    O'Connor-McCourt, M.6
  • 76
    • 84881110695 scopus 로고    scopus 로고
    • Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks
    • Wang E, Zou J, Zaman N, Beitel LK, Trifiro M, Paliouras M. Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks. Semin Cancer Biol. 2013; 23:279-285.
    • (2013) Semin Cancer Biol. , vol.23 , pp. 279-285
    • Wang, E.1    Zou, J.2    Zaman, N.3    Beitel, L.K.4    Trifiro, M.5    Paliouras, M.6
  • 77
    • 84881088550 scopus 로고    scopus 로고
    • Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance
    • Wang E, Zou J, Zaman N, Beitel LK, Trifiro M, Paliouras M. Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance. Semin Cancer Biol. 2013; 23:286-292.
    • (2013) Semin Cancer Biol. , vol.23 , pp. 286-292
    • Wang, E.1    Zou, J.2    Zaman, N.3    Beitel, L.K.4    Trifiro, M.5    Paliouras, M.6
  • 78
    • 84919674249 scopus 로고    scopus 로고
    • Cancer modeling and network biology: accelerating toward personalized medicine
    • Masoudi-Nejad A, Wang E. Cancer modeling and network biology: accelerating toward personalized medicine. Semin Cancer Biol. 2015; 30:1-3.
    • (2015) Semin Cancer Biol. , vol.30 , pp. 1-3
    • Masoudi-Nejad, A.1    Wang, E.2
  • 79
    • 80054881553 scopus 로고    scopus 로고
    • Gaussian interaction profile kernels for predicting drug-target interaction
    • van Laarhoven T, Nabuurs SB, Marchiori E. Gaussian interaction profile kernels for predicting drug-target interaction. Bioinformatics. 2011; 27:3036-3043.
    • (2011) Bioinformatics. , vol.27 , pp. 3036-3043
    • van Laarhoven, T.1    Nabuurs, S.B.2    Marchiori, E.3


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