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Research Paper

GLNMDA: a novel method for miRNA-disease association prediction based on global linear neighborhoods

, ORCID Icon, , ORCID Icon, &
Pages 1215-1227 | Received 21 May 2018, Accepted 24 Aug 2018, Published online: 23 Sep 2018

References

  • Ardekani AM, Naeini MM. The role of micrornas in human diseases. Avicenna J Med Biotechnol. 2010 Oct;2(4):161–179. PubMed PMID: 23407304; PubMed Central PMCID: PMC3558168.
  • Miska EA. How microRNAs control cell division, differentiation and death. Curr Opin Genet Dev. 2005 Oct;15(5):563–568. . PubMed PMID: 16099643.
  • Iorio MV, Ferracin M, Liu CG, et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005 Aug 15;65(16):7065–7070. PubMed PMID: 16103053.
  • Ambros V. The functions of animal microRNAs. Nature. 2004 Sep 16;431(7006):350–355. . PubMed PMID: 15372042.
  • Tang W, Wan SX, Yang Z, et al. Tumor origin detection with tissue-specific miRNA and DNA methylation markers. Bioinformatics. 2018 Feb 1;34(3):398–406. PubMed PMID: WOS:000423978700006; English.
  • Blenkiron C, Goldstein LD, Thorne NP, et al. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol. 2007;8(10):R214. . PubMed PMID: 17922911; PubMed Central PMCID: PMC2246288
  • Zhang X, Zhang X, Wang T, et al. MicroRNA-26a is a key regulon that inhibits progression and metastasis of c-Myc/EZH2 double high advanced hepatocellular carcinoma. Cancer Lett. 2018;426:98–108. . PubMed PMID: WOS:000432877900011; English
  • Zeng X, Zhang X, Zou Q. Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks. Brief Bioinform. 2016 Mar;17(2):193–203. . PubMed PMID: 26059461.
  • Tang W, Liao ZJ, Zou Q. Which statistical significance test best detects oncomiRNAs in cancer tissues? An exploratory analysis. Oncotarget. 2016 Dec 20;7(51):85613–85623. . PubMed PMID: WOS:000391353200147; English.
  • Chen X, Yan CC, Zhang X, et al. Long non-coding RNAs and complex diseases: from experimental results to computational models. Brief Bioinform. 2017 Jul;18(4):558–576. PubMed PMID: WOS:000405717400002; English.
  • Liao ZJ, Li DP, Wang XR, et al. Cancer diagnosis through isomir expression with machine learning method. Curr Bioinf. 2018;13(1):57–63. PubMed PMID: WOS:000425531200008; English.
  • Lu M, Zhang Q, Deng M, et al. An analysis of human microRNA and disease associations. Plos One. 2008;3(10):e3420. . PubMed PMID: 18923704; PubMed Central PMCID: PMCPMC2559869.
  • Zou Q, Li JJ, Song L, et al. Similarity computation strategies in the microRNA-disease network: a survey. Brief Funct Genomics. 2016 Jan;15(1):55–64. PubMed PMID: WOS:000370155900008; English.
  • Jiang Q, Hao Y, Wang G, et al. Prioritization of disease microRNAs through a human phenome-microRNAome network. Bmc Syst Biol. 2010 May 28;4(Suppl 1):S2. PubMed PMID: 20522252; PubMed Central PMCID: PMCPMC2880408. English.
  • Xu J, Li CX, Lv JY, et al. Prioritizing candidate disease miRNAs by topological features in the miRNA target-dysregulated network: case study of prostate cancer. Mol Cancer Ther. 2011 Oct;10(10):1857–1866. PubMed PMID: 21768329.
  • Xuan P, Han K, Guo M, et al. Prediction of microRNAs associated with human diseases based on weighted k most similar neighbors. Plos One. 2013 Aug 8;8(8):e70204. PubMed PMID: 23950912; PubMed Central PMCID: PMCPMC3738541. English.
  • Chen X, Yan CC, Zhang X, et al. HGIMDA: heterogeneous graph inference for miRNA-disease association prediction. Oncotarget. 2016 Oct 4;7(40):65257–65269. PubMed PMID: WOS:000387281000057; English.
  • Shi H, Xu J, Zhang G, et al. Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. Bmc Syst Biol. 2013 Oct;8(7):101. . PubMed PMID: 24103777; PubMed Central PMCID: PMCPMC4124764. English.
  • Chen X, Yan CC, Zhang X, et al. WBSMDA: within and between score for miRNA-disease association prediction. Sci Rep. 2016 Feb;16(6):21106. . PubMed PMID: 26880032; PubMed Central PMCID: PMCPMC4754743. English.
  • Sun DD, Li A, Feng HQ, et al. NTSMDA: prediction of miRNA-disease associations by integrating network topological similarity. Mol Biosyst. 2016;12(7):2224–2232. . PubMed PMID: WOS:000378395000020; English.
  • You ZH, Huang ZA, Zhu Z, et al. PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction. Plos Comput Biol. 2017 Mar;13(3):e1005455. PubMed PMID: 28339468; PubMed Central PMCID: PMCPMC5384769. English.
  • Chen X, Wang LY, Huang L. NDAMDA: network distance analysis for MiRNA-disease association prediction. J Cell Mol Med. 2018 May;22(5):2884–2895. . PubMed PMID: WOS:000430392700032; English.
  • Jiang QH, Wang GH, Jin SL, et al. Predicting human microRNA-disease associations based on support vector machine. Int J Data Min Bioin. 2013;8(3):282–293. . PubMed PMID: WOS:000324166600002; English.
  • Chen X, Yan CC, Zhang X, et al. RBMMMDA: predicting multiple types of disease-microRNA associations. Sci Rep. 2015 Sep;8(5):13877. . PubMed PMID: 26347258; PubMed Central PMCID: PMCPMC4561957. English.
  • Zou Q, Li J, Hong Q, et al. Prediction of MicroRNA-disease associations based on social network analysis methods. Biomed Res Int. 2015;2015:810514. . PubMed PMID: 26273645; PubMed Central PMCID: PMCPMC4529919. English
  • Liu YS, Zeng XX, He ZY, et al. Inferring MicroRNA-disease associations by random walk on a heterogeneous network with multiple data sources. Ieee Acm T Comput Bi. 2017 Jul-Aug;14(4):905–915. PubMed PMID: WOS:000407464700014; English.
  • Li JQ, Rong ZH, Chen X, et al. MCMDA: matrix completion for MiRNA-disease association prediction. Oncotarget. 2017 Mar 28;8(13):21187–21199. PubMed PMID: WOS:000397642400057; English.
  • Chen X, Wu QF, Yan GY. RKNNMDA: ranking-based KNN for MiRNA-disease association prediction. Rna Biology. 2017;14(7):952–962. . PubMed PMID: WOS:000407258600015; English.
  • Chen X, Niu YW, Wang GH, et al. MKRMDA: multiple kernel learning-based Kronecker regularized least squares for MiRNA-disease association prediction. J Transl Med. 2017 Dec 12;15(1):251. PubMed PMID: 29233191; PubMed Central PMCID: PMCPMC5727873. English.
  • Chen X, Huang L. LRSSLMDA: laplacian regularized sparse subspace learning for mirna-disease association prediction. Plos Comput Biol. 2017 Dec;13(12):e1005912. . PubMed PMID: 29253885; PubMed Central PMCID: PMCPMC5749861. English.
  • Xiao Q, Luo JW, Liang C, et al. A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations. Bioinformatics. 2018 Jan 15;34(2):239–248. PubMed PMID: WOS:000419593000008; English.
  • Zeng XX, Liu L, Lu LY, et al. Prediction of potential disease-associated microRNAs using structural perturbation method. Bioinformatics. 2018 Jul 15;34(14):2425–2432. PubMed PMID: WOS:000438248700012; English.
  • Chen X, Huang L, Xie D, et al. EGBMMDA: extreme gradient boosting machine for mirna-disease association prediction. Cell Death Dis. 2018 Jan 5;9(1):3. PubMed PMID: 29305594; PubMed Central PMCID: PMCPMC5849212. English.
  • Chen X, Zhou Z, Zhao Y, ELLPMDA: ensemble learning and link prediction for miRNA-disease association prediction. RNA Biol. 2018 May 25:1–12. DOI:10.1080/15476286.2018.1460016. PubMed PMID: 29619882.
  • Chen X, Xie D, Wang L, et al. BNPMDA: bipartite network projection for miRNA-disease association prediction. Bioinformatics. 2018 Apr 25. DOI:10.1093/bioinformatics/bty333. PubMed PMID: 29701758.
  • Li Y, Qiu CX, Tu J, et al. HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 2014 Jan;42(D1):D1070–D1074. PubMed PMID: WOS:000331139800157; English.
  • Wong TT. Performance evaluation of classification algorithms by k-fold and leave-one-out cross validation. Pattern Recogn. 2015 Sep;48(9):2839–2846. . PubMed PMID: WOS:000356112400007; English.
  • Linden A. Measuring diagnostic and predictive accuracy in disease management: an introduction to receiver operating characteristic (ROC) analysis. J Eval Clin Pract. 2006 Apr;12(2):132–139. . PubMed PMID: 16579821.
  • Yang Z, Wu LC, Wang AQ, et al. dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers. Nucleic Acids Res. 2017 Jan 4;45(D1):D812–D818. PubMed PMID: WOS:000396575500113; English.
  • Jiang Q, Wang Y, Hao Y, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009 Jan;37(Database issue):D98–104. PubMed PMID: 18927107; PubMed Central PMCID: PMCPMC2686559.
  • Das SS, Saha P, Chakravorty N. miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions. Database (Oxford). 2018 Jan 1;2018. doi:10.1093/database/bay023. PubMed PMID: 29688364; PubMed Central PMCID: PMCPMC5829561. English.
  • Ruepp A, Kowarsch A, Schmidl D, et al. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010 Jan 20;11(1):R6. PubMed PMID: 20089154; PubMed Central PMCID: PMCPMC2847718. English.
  • Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 2006 Mar;9(3):189–198. PubMed PMID: 16530703.
  • Yu SL, Chen HY, Chang GC, et al. MicroRNA signature predicts survival and relapse in lung cancer. Cancer Cell. 2008 Jan;13(1):48–57. PubMed PMID: 18167339.
  • Walker S. Updates in small cell lung cancer treatment. Clin J Oncol Nurs. 2003 Sep-Oct;7(5):563–568. . PubMed PMID: 14603554.
  • Raponi M, Dossey L, Jatkoe T, et al. MicroRNA classifiers for predicting prognosis of squamous cell lung cancer. Cancer Res. 2009 Jul 15;69(14):5776–5783. PubMed PMID: 19584273.
  • Seike M, Goto A, Okano T, et al. MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12085–12090. PubMed PMID: 19597153; PubMed Central PMCID: PMCPMC2715493.
  • Patnaik SK, Kannisto E, Knudsen S, et al. Evaluation of microRNA expression profiles that may predict recurrence of localized stage i non-small cell lung cancer after surgical resection. Cancer Res. 2010 Jan 1;70(1):36–45. PubMed PMID: WOS:000278404300007; English.
  • Croce CM. Causes and consequences of microRNA dysregulation in cancer. Eur J Cancer. 2012 Jul;48:S8–S9. PubMed PMID: WOS:000313036500033; English.
  • Inamura K, Ishikawa Y. MicroRNA In Lung Cancer: novel biomarkers and potential tools for treatment. J Clin Med. 2016 Mar 9;5(3). DOI:10.3390/jcm5030036 PubMed PMID: 27005669; PubMed Central PMCID: PMCPMC4810107. English.
  • Fm Q, Yang L, Xx L, et al. Sequence variation in mature microRNA-499 confers unfavorable prognosis of lung cancer patients treated with platinum-based chemotherapy. Clin Cancer Res. 2015 Apr 1;21(7):1602–1613. PubMed PMID: WOS:000352076700015; English.
  • Zhu XX, Zhang X, Wang HF, et al. MTA1 gene silencing inhibits invasion and alters the microRNA expression profile of human lung cancer cells. Oncol Rep. 2012 Jul;28(1):218–224. PubMed PMID: WOS:000304638900031; English.
  • Murakami Y, Yasuda T, Saigo K, et al. Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene. 2006 Apr 20;25(17):2537–2545. PubMed PMID: 16331254.
  • Su H, Yang JR, Xu T, et al. MicroRNA-101, down-regulated in hepatocellular carcinoma, promotes apoptosis and suppresses tumorigenicity. Cancer Res. 2009 Feb 1;69(3):1135–1142. PubMed PMID: 19155302.
  • Li N, Fu H, Tie Y, et al. miR-34a inhibits migration and invasion by down-regulation of c-Met expression in human hepatocellular carcinoma cells. Cancer Lett. 2009 Mar 8;275(1):44–53. PubMed PMID: 19006648.
  • Al-Hajj M, Wicha MS, Benito-Hernandez A, et al. Prospective identification of tumorigenic breast cancer cells. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3983–3988. PubMed PMID: 12629218; PubMed Central PMCID: PMCPMC153034.
  • Pastrello C, Polesel J, Della Puppa L, et al. Association between hsa-mir-146a genotype and tumor age-of-onset in BRCA1/BRCA2-negative familial breast and ovarian cancer patients. Carcinogenesis. 2010 Dec;31(12):2124–2126. PubMed PMID: WOS:000284953900013; English.
  • Ogino S, Giannakis M. Immunoscore for (colorectal) cancer precision medicine. Lancet. 2018 May 26;391(10135):2084–2086. . PubMed PMID: WOS:000433257200007; English.
  • Han Y, Kuang YT, Xue XF, et al. NLK, a novel target of miR-199a-3p, functions as a tumor suppressor in colorectal cancer. Biomed Pharmacother. 2014 Jun;68(5):497–505. PubMed PMID: WOS:000342667800001; English.
  • Siegel RL, Miller KD, Jemal A. Cancer Statistics, 2017. Ca-Cancer J Clin. 2017 Jan-Feb;67(1):7–30. . PubMed PMID: WOS:000393807800003; English.
  • Watanabe A, Tagawa H, Yamashita J, et al. The role of microRNA-150 as a tumor suppressor in malignant lymphoma. Leukemia. 2011 Aug;25(8):1324–1334. PubMed PMID: WOS:000293778900012; English.
  • Wang D, Wang JA, Lu M, et al. Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases. Bioinformatics. 2010 Jul 1;26(13):1644–1650. PubMed PMID: WOS:000278967500010; English.
  • Qu Y, Zhang HX, Liang C, et al. KATZMDA: prediction of miRNA-disease associations based on katz model. Ieee Access. 2018;6:3943–3950. . PubMed PMID: WOS:000426286900001; English
  • Zhang W, Qu QL, Zhang YQ, et al. The linear neighborhood propagation method for predicting long non-coding RNA - protein interactions. Neurocomputing. 2018 Jan;17(273):526–534. . PubMed PMID: WOS:000414762100049; English.
  • Zhang W, Chen Y, Li D. Drug-target interaction prediction through label propagation with linear neighborhood information. Molecules. 2017 Nov 25;22(12). DOI:10.3390/molecules22122056 PubMed PMID: 29186828; English.
  • Zhu L, Shen JL, Xie L, et al. Unsupervised topic hypergraph hashing for efficient mobile image retrieval. Ieee T Cybernetics. 2017 Nov;47(11):3941–3954. PubMed PMID: WOS:000413003100037; English.
  • Zhu L, Shen JL, Jin H, et al. Landmark classification with hierarchical multi-modal exemplar feature. Ieee T Multimedia. 2015 Jul;17(7):981–993. PubMed PMID: WOS:000356522300006; English.
  • Wong KC. MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences. Bioinformatics. 2017 Oct 1;33(19):3028–3035. PubMedPMID: WOS:000411514100008; English.
  • Nepusz T, Yu HY, Paccanaro A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 2012 May 9;5:471–U81. PubMed PMID: WOS:000303544800024; English.
  • Li Y, Liang C, Wong KC, et al. Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. Bioinformatics. 2014 Sep 15;30(18):2627–2635. PubMed PMID: WOS:000342913000012; English.