Journal of Environmental Biology

Analyzing SCID-linked genes with gene set enrichment methods

S. Vasishta¹, C. Sravana Deepthi², Ramya Ramakrishnan³*, B.S. Srinivas¹ and U. Adiga¹     

¹Department of Biochemistry, Apollo Institute of Medical Sciences and Research Chittoor, Murukambattu-517 127, India

²Department of Community Medicine, Apollo Institute of Medical Sciences and Research Chittoor, Murukambattu-517127, India

³Department of General Surgery, Apollo Institute of Medical Sciences and Research Chittoor, Murukambattu-517 127, India

Received: 29 November 2025                   Revised: 04 May 2026                   Accepted: 30 May 2026

*Corresponding Author Email: ramya_rk@aimsrchittoor.edu.in                  *ORCiD: https://orcid.org/0000-0003-3634-1184

Abstract

Aim: Severe Combined Immunodeficiency (SCID) is a life-threatening genetic disorder characterised by profound lymphocyte dysfunction. Despite its prevalence among Indian children, molecular-level understanding remains limited. This study examined the functional properties, pathways, regulatory mechanisms, metabolite interactions, and protein–protein interaction networks of SCID-associated genes.

Methodology: SCID-associated genes retrieved from GeneCards were analysed via Enrichr. Gene Ontology (GO) 2025 defined molecular functions, biological processes, and cellular components. Reactome 2024 identified pathway interactions, ChEA predicted transcription factor binding, HMDB mapped metabolite associations, and STRING facilitated protein–protein interaction (PPI) network construction. Statistical significance was set at p < 0.05.

Results: Key genes identified included RPS3, CTNNB1, RELA, CALR, RPS27A, APP, EEF1A1, HSP90AA1, HSPA8 and NPM1. These were predominantly enriched in protein homeostasis, cell survival, and intracellular organelle function pathways. Transcription factor analysis revealed regulatory elements governing gene expression, whilst metabolite and PPI analyses uncovered coordinated molecular interactions contributing to SCID pathogenesis.

Interpretation: This integrative bioinformatic analysis provides a comprehensive molecular perspective of SCID, spanning gene function to protein interactions, and proposes promising therapeutic targets and molecular markers warranting experimental validation.

Key words: Bioinformatics, Gene enrichment, Gene ontology, Haemopoietic stem cell transplantation, Immune system disorders, Severe combined immunodeficiency

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