همایش ملی بیوانفورماتیک ایران

صفحه اصلی / 4th international edition and 13th Iranian Conference on Bioinformatics

Analysis of enrichment pathways and ontology of genes related to Feed efficiency in sheep

نویسندگان :

Mehre Mohammadnezhad¹ Mohsen Gholizadeh²

1- Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran 2- Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

کلمات کلیدی :

Feed efficiency،Protein-protein interaction network،Gene Ontology،Sheep،Signaling pathway

چکیده :

Feed efficiency is a very important economic feature in animal husbandry. In other words, improving feed efficiency increases profitability for producers (Lin et al., 2023). The purpose of this study was to investigate protein-protein interactions, identify sub-clusters with high density and analyze signaling pathways and gene ontology. For this purpose, a list of 20 genes, which are significantly involved in biological processes related to feed efficiency in sheep, was extracted from different studies. The program String 1.5.1 was used to draw the network of protein-protein interactions (PPI). after, through the more option in the String 1.5.1 program, the created interactive network was expanded to 59 nodes and 394 edges. MCODE 1.6.1 plugin of Cytoscape 3.7.1 software was used to identify high density regions in sub-clusters (Saberi Anvar et al., 2018). MCODE parameters including degree cutoff: 2, node cutoff: 0.2, K-core: 5 and maximum depth: 100 were considered. This calculation led to the creation of five sub-clusters. In the subcluster with the highest score: 14/421, nodes: 20, edges: 137 and a seed protein named ACACA was identified. Acetyl-CoA carboxylase alpha is considered as the rate-limiting enzyme in the biosynthesis of various fatty acids in lipid metabolism (Ntambi et al., 2002). Also, LEP protein with a member score of 38 in the main network and sub-cluster as the main protein (hub) had the highest degree in the PPI network. The hormone leptin secreted in adipose tissue plays an important role in regulating appetite and energy metabolism. In addition, leptin is associated with fat deposition. After leptin protein binds to the receptor, it creates a series of chemical signals (JAK/STAT signaling pathway) that activates the receptor and trans phosphorylates the associated JAK molecules. This pathway participates in energy homeostasis. The LEP gene is a component of several biological processes, especially those related to fat metabolism, such as the lipid metabolic process and beta-oxidation of fatty acids (Stern et al., 2016). The leptin also plays a vital role in biological processes that are related to the negative regulation of appetite, feeding behavior, intestinal absorption, and bone growth in sheep (Upadhyay et al., 2015). ClueGO 2.5.10 and CluePedia 1.5.10 plugins were used to draw the gene ontology network (Bindea et al., 2013). After analysis, significant (P<0.05) gene ontology terms including molecular functions of insulin-like growth factor I binding, insulin-like growth factor II binding, insulin-like growth factor binding, hormonal activity, triglyceride lipase activity and biological processes such as insulin-like growth factor receptor signaling pathway, positive regulation of MAPK cascade, positive regulation of receptor signaling pathway via JAK-STAT, brown fat cell differentiation, muscle organ development, skeletal muscle cell differentiation, glucose homeostasis and response to insulin were identified. It was also found that these genes are significantly related to KEGG enrichment pathways such as AMPK signaling pathway, PPAR signaling pathway, Regulation of lipolysis in adipocytes, Growth hormone synthesis, secretion and action, PI3K-Akt signaling pathway and Insulin signaling pathway.