A meta-analysis of differentially expressed and regulatory genes with their functional enrichment analysis for brain transcriptome data in autism spectrum disorder

Abstract

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by persistent challenges in social interactions and repetitive behavioral patterns. It is a significant problem emerging worldwide, as one in 100 children is affected by this disorder globally. In this study, a meta-analysis was performed for the identification of differentially expressed genes (DEGs) along with the expression analysis of regulatory genes. Functional enrichment analysis was an integral part of current findings to notify the significant pathways of this complex disorder. The study was conducted with two RNA-Seq datasets, viz., GSE64018 and GSE62098, for ASD patients and control samples from the GEO database. The identification of up-regulatory and down-regulatory genes was performed by the interaction analysis of transcription factors (TF) and DEGs. As an outcome of the meta-analysis, 2543 DEGs were identified as common across both of the datasets in which 1402 DEGs exhibited upregulation and 1130 genes have shown downregulation. In network analysis, upregulatory genes have shown strong interaction while downregulatory genes exhibit weak or null interaction. Further, in the enrichment analysis of screened upregulatory DEGs, three major significant pathways were identified namely the ATP synthesis pathway, FAS signaling pathway, and the Huntington’s disease pathway. The common expression of CYC 1 gene in all the identified pathways has indicated that it is an important key regulator gene for the majorly associated pathways. The study concludes that all the potential DEGs were found to show their related high expression in neurobiological regulations specifically with ASD.

Communicated by Ramaswamy S. Sarma

Keywords:

• Autism spectrum disorder
• differentially expressed genes
• meta-analysis
• RNA Seq
• functional enrichment analysis

Disclosure statement

The authors declare that they have no conflict of interest and no financial interest is involved in this study.

Funding

The author(s) reported there is no funding associated with the work featured in this article.

Data availability statement

The datasets that support the findings of this study are openly available in NCBI Gene Expression Omnibus Database at https://www.ncbi.nlm.nih.gov/geo (Gandal et al., 2018; Takumi et al., 2020).