AutDB: a gene reference resource for autism research

Abstract

Recent advances in studies of Autism Spectrum Disorders (ASD) has uncovered many new candidate genes and continues to do so at an accelerated pace. To address the genetic complexity of ASD, we have developed AutDB (http://www.mindspec.org/autdb.html), a publicly available web-portal for on-going collection, manual annotation and visualization of genes linked to the disorder. We present a disease-driven database model in AutDB where all genes connected to ASD are collected and classified according to their genetic variation: candidates identified from genetic association studies, rare single gene mutations and genes linked to syndromic autism. Gene entries are richly annotated for their relevance to autism, along with an in-depth view of their molecular functions. The content of AutDB originates entirely from the published scientific literature and is organized to optimize its use by the research community. The main focus of this resource is to provide an up-to-date, annotated list of ASD candidate genes in the form of reference dataset for interrogating molecular mechanisms underlying the disorder. Our model for consolidated knowledge representation in genetically complex disorders could be replicated to study other such disorders.

Figure 1.

(A) An integrated model for collection, annotation, storage and visualization of candidate genes for ASD. (1) Candidate genes for ASD are compiled and maintained from an exhaustive search of scientific literature in the PubMed database maintained at NCBI (2) ASD candidates are classified into four categories. (3) Entries are organized in the database for search and retrieval. (4) User-friendly display of candidate genes at two levels for display and easy access with links to various external databases. (B) Search and display of candidate genes in AutDB. A search box is used to retrieve ASD candidate genes catalogued in AutDB using various gene attributes. The search results are displayed at two levels. At level 1, the gene entry is displayed in the summary row format showing: (A) gene symbol, (B) gene name, (C) chromosomal location, (D) Genetic category, (E) GAD and (F) OMIM links where available, (G) Number of autism-specific studies, (H) primary PubMed reference and (I) detail/edit button. A level 2, the entry is further displayed at a detail level in three-tier format showing: (1) gene summary with links to external databases such as Entrez Gene and UniProt, (2) relevance for autism displaying candidate gene report summary and (3) references arranged under three sub-headings: references for the candidate gene reports, highly referred and recent studies of the candidate genes.

Figure 2.

Online display of AutDB search results. (A) Searching for candidate genes on Chromosome 2 retrieved an annotated list of ASD candidate genes in Chromosome 2.