Supplementary Material for: An Integrative in silico Study to Discover Key Drivers in Pathogenicity of Focal and Segmental Glomerulosclerosis

Background FSGS (focal and segmental glomerulosclerosis) is a clinical-pathologic condition marked by segmental and localized glomerular damages. Despite investigations, the molecular mechanisms behind FSGS development remain to be more clarified. By a comprehensive analysis of a FSGS related array set, the aim of this study was to unravel the top pathways and molecules involved in the pathogenesis of this disorder. Methods FSGS related microarray dataset (GSE129973) from the Gene Expression Omnibus (GEO) database was quality checked, analyzed and its differentially expressed genes (DEGs) (log2FC>1) were used for construction of a protein-protein interaction (PPI) network (STRING). The degree of centrality was considered to select the hub molecules in the network. The WGCNA was utilized to construct co-expression modules. Hub molecules were selected based on module membership (MM) and gene significant (GS) values in the disease’s most correlated module. After spotting the key molecules considering both strategies, their expression pattern were checked in other FSGS microarray datasets. Gene ontology (GO) and Reactome pathway enrichment analyses were performed on the DEGs of the related module. Results After quality checking, normalization and analysis of the dataset, 5296 significant DEGs including 2469 up-regulated and 2827 downregulated DEGs were identified. The WGCNA algorithm clustered the DEGs into nine independent co-expression modules. The disease most-correlated module (black module) was recognized and considered for further enrichment analysis. The immune system, cell cycle, and vesicle-mediated transports were among the top enriched terms for the identified module’s DEGs. The immune system, cell cycle, and vesicle-mediated transports were among the top enriched terms for the black module’s DEGs. The key molecules (BMP-2 and COL4A1) were identified as common hub molecules extracted from the two methods of PPI and the co-expressed networks. The two identified key molecules were validated in other FSGS datasets, where a similar pattern of expression was observed for both the genes. Conclusions Two hub molecules (BMP-2 and COL4A) and some pathways (vesicle-mediated transport) were recognized as potential players in the pathogenesis of FSGS.