dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder

Abstract

Background: Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed.

Methods: Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples). Then, we applied R language software and developed an interactive shared and updated database (dbMDEGA) displaying the results of meta-analysis of data from ASD studies regarding differentially expressed genes (DEGs) in the brain.

Results: This database, dbMDEGA ( https://dbmdega.shinyapps.io/dbMDEGA/ ), is a publicly available web-portal for manual annotation and visualization of DEGs in the brain from data from ASD studies. This database uniquely presents meta-analysis values and homologous forest plots of DEGs in brain tissues. Gene entries are annotated with meta-values, statistical values and forest plots of DEGs in brain samples. This database aims to provide searchable meta-analysis results based on the current reported brain gene expression datasets of ASD to help detect candidate genes underlying this disorder.

Conclusion: This new analytical tool may provide valuable assistance in the discovery of DEGs and the elucidation of the molecular pathogenicity of ASD. This database model may be replicated to study other disorders.

Keywords: Database; Gene expression; Meta-analysis; Microarray.

Fig. 1

A flow diagram for the collection, annotation and presentation of associated genes for ASD. (1) The data in this database were obtained from our meta-analysis results and gene expression datasets of human and mouse ASD studies obtained from GEO DataSets (http://www.ncbi.nlm.nih.gov/gds). (2) Gene entry is organized for searching in the database. (3) The developed database is presented

Fig. 2

Online display of dbMDEGA search results. The example shows retrieval of a candidate gene, ITPR1, in dbMDEGA, (a) The meta-analysis results for male cortex together with three forest plots (for human male cortex samples; for human cerebellum samples; and for male, female and formalin fixed cortex) are displayed. b The statistical values of the candidate gene in one human dataset and a bean plot of the cases and controls are presented. c The candidate gene is also annotated with three forest plots of 14 mouse ASD model studies