Pathway enrichment and network analysis of differentially expressed genes in pashmina goat

Abstract

Gene expression, pathway analysis and cellular processes in Pashmina goat helps to understand the dynamics and production mechanisms of its long-fibre and in propagating its valued traits to other goat breeds. We obtained 8418 DEGs (p-value cutoff for FDR < 0.001 and log2FC > 2) from our previous differential expression analysis of Pashmina and Barbari goats. Here, out of the aforementioned total, 152 up-regulated (TMM ≥ 100) and 919 down-regulated genes (TMM 1 < 0) were searched for key GO enriched terms and pathways with the Benjamini p-value <0.05. These were further mapped to STRING database for acquiring protein-protein interaction (PPI) networks. The enriched biological processes with significant Padj values comprise skin development, keratinocyte differentiation and filament regulation. The molecular functions performed by down-regulated genes with highest Padj values are protein binding and GTPase regulator activity while others are present in microtubule cytoskeleton thus providing the structural or functional support. The adhesion molecules, calcium-binding genes, KRTs, KRTAPs, and collagen molecules exhibited maximum interactions that all serve as key regulators in hair growth. The maximum interaction exhibited by down-regulated genes in PPI network is involved in binding of ions, microtubule organization, development and replication processes. Implication of this whole computational framework makes it feasible to highlight the relevant genes and their functional interactive networks. The highly enriched terms may further be explored with inclusion of more samples for improving the quality of the analysis and how genetics, breeding, feeding and even husbandry practices may modulate these pathways for better productivity.