SFARI Gene 3.0 User Guide

The User Guide is designed to acquaint new users with SFARI Gene, an integrated resource for autism research, and provide them with a quick and efficient pathway to the information about ASD-candidate genes that’s most pertinent to their work.

This document features step-by-step instructions for using the Human Gene, Animal Model, Copy Number Variant, Protein Interaction, and Gene Scoring modules of SFARI Gene, as well as a detailed introduction to our new data visualization tools, the Human Gene Scrubber, the Copy Number Variant (CNV) Scrubber, and the Ring Browser. It also provides instructions for citing SFARI Gene.

Please feel free to contact us with any comments or questions about the database.

Getting Started

Welcome to SFARI Gene.

We hope that you benefit from this publicly available, curated, web-based, searchable database for autism research. SFARI Gene contains interactive modules linking information about risk genes for autism with corresponding data from peer-reviewed research on human genes, animal models, and more.

Human Gene Module

The Human Gene module is an active collection of candidate genes identified through genetic association studies, genes linked to syndromic autism, and genes in which rare mutations have been found that are linked to autism.

CNV

The Copy Number Variant (CNV) module of SFARI Gene is a comprehensive, up-to-date collection of all known CNVs that have been associated with ASD. CNVs are segments of DNA, typically greater than 1,000 basepairs in length, that vary in number from person to person. These submicroscopic deletions and duplications are increasingly thought to be involved in the pathogenesis of a wide range of human diseases, including neuropsychiatric disorders such as ASD. For this reason, the CNV module of SFARI Gene serves as a valuable resource for the ASD research community.

Animal Models Module

The Animal Models module of SFARI Gene examines data from animal models used in laboratory research to elucidate the mechanisms of action of ASD risk genes. Through rigorous curation of primary scientific research, the Animal Models module provides integrated coverage of the latest discoveries at the molecular, cellular, and behavioral levels in ASD.

PIN

The Protein Interaction (PIN) module of SFARI Gene is an interactive visual reference that showcases all known protein interactions of gene products associated with ASD. It includes six major types of protein-protein and protein-nucleic acid interactions: protein binding, RNA binding, promoter binding, protein modification, autoregulation, and direct regulation. Each protein interaction is manually curated from primary reference articles after consultation with public databases (BioGRID, HPRD, PubMed) and commercial resources (Pathway Studio 7.1). The PIN module is designed to help accelerate ASD research by acting as a bioinformatics platform for network biology analysis of the molecular pathways underlying ASD pathogenesis.

Ring Browser

The Ring Browser allows users to see an overview of the human genetic information contained in the SFARI Gene database. With its unique circular interface, the Ring Browser can be used to show the location and frequency of ASD candidate genes, CNVs, and protein interactions along the entirety of the human genome.

The interactive Ring Browser tool is capable of displaying data from many different SFARI Gene modules.

Glossary

To help our users better understand the data contained within SFARI Gene, we have created a glossary defining some of the most common terms found throughout the database. The glossary will help contextualize information for users as they explore the website.

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