'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration

Abstract

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/.

Figure 1.

Flowchart of the procedure for ‘RetinoGenetics’. ‘RetinoGenetics’ mainly consists of three parts: (i) data extraction based on publication search, (ii) mutation annotation of all variants and genes using ANNOVAR and (iii) enrichment analysis with all IRD-related genes by WebGestalt and network analysis graphically showing intrinsic relations between genes and phenotypes.

Figure 2.

A screenshot of the browse and search tools in ‘RetinoGenetics’. ‘Browse by chromosome’ is used to retrieve all IRD-related genes mapped on chromosomes, and each is linked to ‘Gene report’. ‘Browse by disease’, ‘Browse all’ and ‘Search’ aim to get ‘Gene list’, through which ‘Gene report’ and ‘Mutation annotation’ can be further obtained. ‘Gene report’ lists a detailed summary of the gene including ‘Mutation spectrum’, whereas ‘Mutation annotation’ displays information like location, clinical phenotype, functional prediction and details in existing databases.