Identification of disease genes and assessment of eye-related diseases caused by disease genes using JMFC and GDLNN

References

• Akmal Remli M, Mohd Daud K, Wen Nies H, Mohamad MS, Deris, S, Omatu S, Kasim S, Sulong G. 2017. K-means clustering with infinite feature selection for classification tasks in gene expression data. In: Shakhovska N, editor. Advances in intelligent systems and computing. Vol. 616. Cham: Springer; p. 50–57.
   Google Scholar
• Balamurugan R, Natarajan AM, Premalatha K. 2016. A modified harmony search method for biclustering microarray gene expression data. IJDMB. 16(4):269–289.
   Google Scholar
• Chen X, Wang L, Qu J, Guan N-N, Li J-Q. 2018. Predicting miRNA-disease association based on inductive matrix completion. Bioinformatics. 34(24):4256–4265.
   PubMed Web of Science ®Google Scholar
• Chen X, Xie D, Zhao Q, You Z-H. 2019. MicroRNAs and complex diseases: from experimental results to computational models. Brief Bioinform. 20(2):515–539.
   PubMed Web of Science ®Google Scholar
• Chen X, Yin J, Qu J, Huang L. 2018. MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction. PLoS Comput Biol. 14(8):e1006418.
   PubMed Web of Science ®Google Scholar
• Chen X, Zhu C-C, Yin J. 2019. Ensemble of decision tree reveals potential miRNA-disease associations. PLoS Comput Biol. 15(7):e1007209.
   PubMed Web of Science ®Google Scholar
• Chuang C-L, Chen CM, Shieh GS, Jiang JA. 2007. GeneCFE-ANFIS a neuro-fuzzy inference system to infer gene-gene interactions based on recognition of microarray gene expression patterns. Biomed Eng Appl Basis Commun. 19(02):71–78.
   Google Scholar
• Domalpally A, Agrón E, Pak JW, Keenan TD, Ferris FL, III, Clemons TE, Chew EY. 2019. Prevalence, risk, and genetic association of reticular pseudodrusen in age-related macular degeneration: Age-related eye disease study 2 report 21. Ophthalmology. 126(12):1659–1666.
   PubMed Web of Science ®Google Scholar
• Gabriel LA, Traboulsi EI. 2011. Genetic diagnostic methods for inherited eye diseases. Middle East Afr J Ophthalmol. 18(1):24–29.
   PubMedGoogle Scholar
• Holt RJ, Young RM, Crespo B, Ceroni F, Curry CJ, Bellacchio E, Bax DA, Ciolfi A, Simon M, Fagerberg CR, et al. 2019. De novo missense variants in fbxw11 cause diverse developmental phenotypes including brain, eye, and digit anomalies. Am J Hum Genet. 105(3):640–657.
   PubMed Web of Science ®Google Scholar
• Horowitz CR, Orlando LA, Slavotinek AM, Peterson J, Angelo F, Biesecker B, Bonham VL, Cameron LD, Fullerton SM, Gelb BD, et al. 2019. The genomic medicine integrative research framework: a conceptual framework for conducting genomic medicine research. Am J Hum Genet. 104(6):1088–1096.
   PubMed Web of Science ®Google Scholar
• Jiang X. 2017. Identification of disease-related genes based on tensor factorization with RNA-seq data of Huntington's disease mice. In Chinese Automation Congress (CAC). Jinan, China: IEEE; p. 26–31.
   Google Scholar
• Jiang Z, Li T, Min W, Qi Z, Rao Y. 2017. Fuzzy c means clustering based on weights and gene expression programming. Pattern Recog Lett. 90:1–7.
   Web of Science ®Google Scholar
• Jimenez JE, Nourbakhsh A, Colbert B, Mittal R, Yan D, Green CL, Nisenbaum E, Liu G, Bencie N, Rudman J, et al. 2020. Diagnostic and therapeutic applications of genomic medicine in progressive, late-onset, nonsyndromic sensorineural hearing loss. Gene. 747:144677.
   PubMed Web of Science ®Google Scholar
• Jowkar G-H, Mansoori EG. 2016. Perceptron ensemble of graph-based positive-unlabeled learning for disease gene identification. Comput Biol Chem. 64:263–270.
   PubMed Web of Science ®Google Scholar
• Jubair S, Qassim Muftin N, Hashim N, Rieyadh S, Saad H. 2019. Investigation of MYOC gene involvement in primary congenital glaucoma in a sample of Iraqi children. Gene Rep. 16:100413.
   Web of Science ®Google Scholar
• Kakrana A, Yang A, Anand D, Djordjevic D, Ramachandruni D, Singh A, Huang H, Ho JWK, Lachke SA. 2018. iSyTE 2.0: a database for expression-based gene discovery in the eye. Nucleic Acids Res. 46(D1):D875–D885.
   PubMed Web of Science ®Google Scholar
• Lage K, Karlberg EO, Størling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tümer Z, Pociot F, Tommerup N, et al. 2007. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol. 25(3):309–316.
   PubMed Web of Science ®Google Scholar
• Liu W, Liu J, Rajapakse JC. 2018. Gene ontology enrichment improves performances of functional similarity of genes. Sci Rep. 8(1):12100–12112.
   PubMedGoogle Scholar
• Mazandu GK, Chimusa ER, Mulder NJ. 2016. Expressions of different semantic similarity measures in the context of biomedical sciences and WordNet. Brief Bioinform (Suppl Mat). 18(5):886–901.
   Google Scholar
• Murugesan V, Balamurugan P. 2019. Disease gene identification using reliable robust classifier. Int J Recent Technol Eng (IJRTE). 7(6):70–74.
   Google Scholar
• Nesterova AP, Klimov EA, Zharkova M, Sozin S, Sobolev V, Ivanikova NV, Shkrob M, Yuryev A. 2021. Diseases of the eye. Adv Protein Chem Struct Biol. 126:279–296.
   PubMed Web of Science ®Google Scholar
• Nikdelfaz O, Jalili S. 2018. Disease genes prediction by HMM based PU-learning using gene expression profiles. J Biomed Inform. 81:102–111.
   PubMed Web of Science ®Google Scholar
• Pragadeesh C, Jeyaraj R, Siranjeevi K, Abishek R, Jeyakumar G. 2021. Hybrid feature selection using micro genetic algorithm on microarray gene expression data. Clin Neurophysiol. 132(9):2152–2246.
   PubMedGoogle Scholar
• Ren X, Wang S, Huang T. 2020. Decipher the connections between proteins and phenotypes. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics. 1868(11):1–7.
   Web of Science ®Google Scholar
• Richardson R, Smart M, Tracey-White D, Webster AR, Moosajee M. 2017. Mechanism and evidence of nonsense suppression therapy for genetic eye disorders. Exp Eye Res. 155:24–37.
   PubMed Web of Science ®Google Scholar
• Rościszewska-Żukowska I, Bartosik-Psujek H. 2020. Optic nerve atrophy and whole and regional brain atrophy in Leber's hereditary optic neuropathy with multiple sclerosis-like disease with m. 11778G > A mutation. Multiple Sclerosis Relat Disord. 42:102071.
   PubMed Web of Science ®Google Scholar
• Samuelov L, Kinori M, Mancini AJ, Kruse LL, Wagner A, Yoon H, Chamlin SL. 2019. Ocular complications in PHACE syndrome: a true association or a coincidence? J Pediatr. 204:214–218.
   PubMed Web of Science ®Google Scholar
• Schmoldt A, Benthe HF, Haberland G. 1975. A new family of similarity measures for scoring confidence of protein interactions using Gene Ontology. Biochem Pharmacol. 24(17):1639–1641.
   Web of Science ®Google Scholar
• Singh M, Tyagi SC. 2018. Genes and genetics in eye diseases: a genomic medicine approach for investigating hereditary and inflammatory ocular disorders. Int J Ophthalmol. 11(1):117–134.
   PubMed Web of Science ®Google Scholar
• Vidal S, Brandi N, Pacheco P, Maynou J, Fernandez G, Xiol C, Pascual-Alonso A, Pineda M, Armstrong J., Rett Working Group. 2019. The most recurrent monogenic disorders that overlap with the phenotype of Rett syndrome. Eur J Paediatr Neurol. 23(4):609–620.
   PubMed Web of Science ®Google Scholar
• Xiao Y, Xu C, Ping Y, Guan J, Fan H, Li Y, Li X. 2011. Differential expression pattern-based prioritization of candidate genes through integrating disease-specific expression data. Genomics. 98(1):64–71.
   PubMed Web of Science ®Google Scholar
• Yang P. 2017. “Computational approaches for disease gene identification”, arXiv preprint arXiv:1704.03548.
   Google Scholar