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A. Tewari, G. Abrams; Integrated Network–Based Bioinformatic Analysis of Genes Involved in Retinitis Pigmentosa and Usher Syndrome . Invest. Ophthalmol. Vis. Sci. 2005;46(13):1803.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose: Extensive genetic analysis of Retinitis Pigmentosa and Usher syndrome have led to the cloning of over 30 genes that predispose to these disorders, with several loci remaining uncloned. The genetic complexity of these conditions suggests that the known genes may function in interconnected networks that support retinal physiology. Our purpose was to use a bioinformatics approach to delineate such networks. Methods: Recent large–scale functional genomic studies have provided data that can be used to build molecular interaction networks. We applied an integrative approach to interrogate relevant genomic databases to derive networks of interactions between established and putative novel genes involved in the pathogenesis of Retinitis Pigmentosa and Usher syndrome. Using the known genes implicated in Retinitis Pigmentosa and Usher syndrome as queries (including ABCA4, CA4, CDH23, CERKL, CNGA1, CNGB1, CRB1, CRX, FSCN2, GUCA1B, IMPDH1, LRAT, MASS1, MERTK, MYO7A, NR2E3, NRL, PCDH15, PDE6A, PDE6B, PRPF3, PRPF8, PRPF31, RDS, RHO, RGR, RLBP1, ROM1, RP1, RP2, RP9, RPE65, RPGR, SAG, SANS, TULP1, USH1C, USH2A, USH3A), we explored protein interaction and gene co–expression data to derive an integrated network of gene/protein interactions that was visualized using Cytoscape network graph drawing software. Results: Our approach defined a complex gene and protein interaction network including both known and many putative novel genes involved in Retinitis Pigmentosa and Usher syndrome. Computational analysis of the network suggests a scale–free structure. The Cytoscape network graph revealed several novel genes that may be good candidates for further genetic analysis. Conclusions: The novel molecular network defined here provides a framework for the further study of the genetic basis of Retinitis Pigmentosa, Usher syndrome, and related retinal diseases.
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