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  • Top 5 genes

    Top 5 diseases

    Data summary

    • Publications : 991
    • Phenotypes : 178
    • Genes : 207
    • Mutations : 4573
    • SNVs : 3404
    • InDels : 1169
    • Last Update : 26/10/2017

    Tutorial


    • Overview

    • RetinoGenetics is a comprehensive mutation database for genes related to inherited retinal degeneration (IRD). It contains such IRD-related genetic factors as SNVs and InDels. Data in this database were derived from both profound literature accessed manually and extended functional annotation, such as ANNOVAR, Gene Ontology (GO), protein interaction network (PPI) and Pathway analysis. A full annotation of each genetic factor was made, and the correlations among these genetic factors were demonstrated to make RetinoGenetics a comprehensive and connected information resource for further genetic studies of IRD. RetinoGenetics provide several ways to search (part 5) for the thought of facilitating users to access data they want. Additionally, browser (part 6) was also incorporated to facilitate browsing.
      In each page, we also provide the guider bar on the top of the page. If you get lost in the page, you may click the up-arrow to the top and click on the guider bar to a new page you like.

    • Data summary

    • At present, the RetinoGenetics database contains a total of 4,310 variants extracted from 943 studies, including 3,175 SNVs and 1,135 InDels. Category statistics of retinal disease related genetic factors were shown in Table 1.

      Table 1 Data content and statistics of IRD-related genetic factors in RetinoGenetics


      Data type                                                                          Data count

      Mutations                              SNVs                                   3,175 (4,310)
                                                    InDels                                 1,135 (4,310)
      Genes                                                                               194
      Phenotypes                                                                      178
      Publications                                                                      943
      Pathways                                                                          39 (p>0.05)
      PPIs                                                                                  17 (p>0.05)
      GO terms                                                                         111 (p>0.05)


    • Data collection

    • We performed a comprehensive search in PubMed for studies related with IRD, and a total of 943 literatures were collected. Details of variants like phenotype, gene symbol, cDNA change, ethnicity were extracted from original publications.

    • Data analysis

      • Enrichment analysis

        • Gene Ontology

        • Gene Ontology annotation, including such three parts as Cellular Component, Molecular Function and Biological Process, was performed by WebGestalt 2.0. Each part contains the GO term accession, GO term name, Ratio of enrichment, P-Value , Adjusted P-value and Genes related. Hyperlinks were provided in column 'Genes related' ( Figure 1 ), which will show detailed information in RetinoGenetics about that gene.

          Figure 1

        • Pathway analysis

        • Enriched pathway information was accessed through WebGestalt 2.0, which includes KEGG analysis, Wikipathways analysis and Pathway commons analysis. Each part contains Term, Ratio of enrichment, P-value, Adjusted P-value and Genes related.

          Figure 2

        • Protein interaction network

        • We peformed protein interaction network module analysis by WebGestalt 2.0. Figure 3 shows the most statistically significant PPI.

          Figure 3
      • Mutation spectrum and gene-disease network

        • Mutation spectrum

        • To graphically display mutations in genes, SVG was used to achieve the visualization of mutation spectrum. Figure 4 shows a demo mutation spectrum.

          Figure 4

        • Gene-disease network

        • To facilitate the exploration of the exceptional genetic heterogeneity of inherited retinal diseases, gene-disease network, implemented by SVG, was completed to graphically and vividly show intrinsic relations between IRD genes and IRD. Figure 5 shows a demo gene-disease network.

          Figure 5

      • Annovar annotation

      • Based on data collected from publications, we performed ANNOVAR analysis, which can generate detailed information of variant, like gene annotation, amino acid change annotation, SIFT scores, PolyPhen scores, LRT scores, MutationTaster scores, PhyloP conservation scores, GERP++ conservation scores, dbSNP identifiers, 1000 Genomes Project allele frequencies, NHLBI-ESP 5400 exome project allele frequencies and other information. Users can get annotations above by clicking hyperlinks in the column 'RetinoGenetics ID'. C2G convertion was used to convert coordinate from CDS to genome.


    • Search

    • Besides the 'Quick Search' provided in the left navigation bar, three search modules, namely, 'Variant Search', 'Disease Search' and 'Batch Search' in the guider bar 'Search' were developed.
      The 'Variant Search' module allows users to search the RetinoGenetics by specifying options like gene region, mutation type, effect or locus to get mutations they want. The 'Disease Search' module can be useful if users want mutations of a specfied phenotype. The 'Batch Search' module maybe helpful when users want data of more than one gene, and a gene symbol list will be needed. A demo quick search is shown in Figure 6. Other three types of search result is similar to quick search result.

      Figure 6

    • Browser

    • To facilitate users to browse the data in RetinoGenetics, three different approaches are provided: (i) browse all; (ii) browse by disease; and (iii) browse by chromosome. The 'browse all' provides five options (chromosome, gene region, mutation type, effect and gene system) for users to retrieve the information of mutations of interest conveniently. Meanwhile, top seven hereditary retinal diseases with the highest number of related mutations are presented. The genes and mutations related to this diseases can be easily retrieved by selecting a listed disease. Additionally, users can browse RetinoGenetics by chromosome in a graphical way, in which all the variants are mapped on the chromosomes and linked to gene information page. Figure 7 shows a demo browser.

      Figure 7