We are delighted to announce the launch of a redesigned version of SFARI Gene. The updated platform features a streamlined user interface, new data visualizations, improved search capability, and, most importantly, a continued commitment to the rigorous and thorough curation users have come to expect.
Current estimates suggest that variation in several hundred different genes could affect susceptibility to autism. SFARI and other funding agencies are supporting efforts to identify as many of these “risk genes” as possible, with an eye toward understanding how mutations in these genes might affect brain development and result in the complex spectrum of behaviors that we collectively call “autism.” Given the scale of the dataset involved, there is a real need in the field for a trusted, comprehensive, and dynamic database that catalogues all known information on these risk genes from the published literature and gives autism researchers immediate access to it.
Since 2008, SFARI Gene has done this by providing:
- An annotated, downloadable list of autism risk genes
- An expert assessment of the strength of the evidence implicating each gene
- An annotated list of copy number variants (CNVs) implicated in autism risk
- A list of available animal models of autism based on the risk genes, along with the most essential and relevant information about the phenotype of each model
- An annotated list of proteins with which the products of the autism risk genes are known to interact
All of this information is carefully curated by the team at MindSpec, updated quarterly, and offered with extensive links to the primary literature and secondary databases.
Our goal in redesigning the site was to enhance the user experience, making it easier for investigators to navigate from module to module to find the information they want as quickly as possible. Along the way, we hope that this wealth of information will promote new hypotheses that can be tested in the lab.
New features of the site include:
- An interactive “gene scrubber” that allows the user to get a genome-wide view of autism risk genes or select smaller regions of the genome to focus on. This visualization provides at-a-glance views of autism risk genes, the number of publications on each, and, crucially, the gene score for each. Additional filters can let users see the number of autism-specific publications for each gene, select particular chromosomes to focus on, or select genes by the gene score they’ve been assigned.
- A redesigned view of all information collected on every individual gene. Clicking on a particular gene, either in the scrubber or in the alphabetized table of genes, leads to a view of in-depth information about the gene that users will be familiar with, plus some new features including a prominently placed gene score, one-click access to the explanation of that score, and a history of any changes made to the score.
- An interactive gene scrubber for the CNV data, similar to the tool offered for the human gene information. This scrubber can be used to view the number of studies for each CNV, the number of CNVs at a particular locus, and by status as either deletion or duplication. High-level information for CNVs can be found by hovering over them in the scrubber window or in the table below the visualization. Clicking on an individual CNV shows median start and end points for each, as well as the full population-level and individual-level dataset, in a clear and readable format.
- An updated animal model module that includes all of the extensive genetic and phenotypic information that users are accustomed to, along with clear links to the human genetic evidence and examples of phenotypic rescues of each model.
- A protein interaction (PIN) module that now includes a genome-wide visualization of interactions between gene products in the database, which can easily be filtered by gene score category and/or by the type of interaction.
The new navigation system and data visualizations are supported by advanced search capability, data download functionality, a glossary of frequently used terms, and an extensively rewritten user guide. This news page will also feature outlines of the quarterly updates to the database.
We are gratified that SFARI Gene is increasingly cited in the primary literature, and we hope the redesigned version of the site will continue to be useful to researchers studying the genetic underpinnings of autism. We look forward to your comments and feedback.