Bioinformatics Approach to Evaluate GRIN2B Gene in Depression–An in silico Study

ABSTRACT

Introduction: The objective of the in silico study was to evaluate GRIN2B gene using bioinformatics tools so as to discover the probable effect of mutations of this gene as well as its protein-protein interactions with the pathobiology of depression. Materials and Methods: In silico analysis of SNPs of GRIN2B gene was conducted using its accession IDs and their FASTA amino acid sequences obtained from NCBI. SIFT, Polyphen-2, CADD score, MetaLR and mutation assessor were the bioinformatics softwares utilized for the study. Protein–protein interaction was assessed by string database. Results:Analysis of SNPs of GRIN2B gene by SIFT revealed 56.42% mutations were tolerated and 43.58% were damaging. Polyphen-2 analysis showed 46.36% SNPs were deleterious and 53.64% were benign mutations. On metaLR analysis, 7.93% of the SNPs found to be dangerous mutations whereas 92.07% of them were tolerated. CADD scores presented 2.67% damaging and 97.32% tolerant mutations of GRIN2B gene. A total of 2.46%, 39.72%, 27.3% and 30.51% of the mutations were found to be high, low, medium and neutral as per the mutation assessor tool. According to a string database analysis, there were 11 nodes, 37 edges (instead of the expected 14 edges), an average node degree of 6.73, and an average local clustering coefficient of 0.79 and protein protein interaction enrichment p-value was 1.018e-07. Conclusion: The results propose that GRIN2B gene mutations that are deleterious and its interactions as obtained by the bioinformatics softwares may have a crucial role the pathogenesis of depression.

KEYWORDS

• GRIN2B
• Bioinformatics
• Gene
• Polymorphism
• Depression
• Protein-protein interaction

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• DOI10.5530/ijpi.13.4.107Copy

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