One systems biology analysis protein-protein interaction of NASH and IBD based on comprehensive gene information
Gastroenterology and Hepatology from Bed to Bench,
5 August 2017
Aim: Analysis reconstruction networks from two diseases, IBD and NASH and their relationship, based on systems biology methods.
Background: IBD and NASH are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on co-existence of these two diseases. In addition, they have some similar risk factors such as age, obesity, and insulin resistance. Therefore, systems biology approach can help to discover their relationship.
Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. Based on degree and Betweenness, hubs and bottleneck nodes were defined.
Results: Common genes between IBD and NASH construct a network with 99 nodes. Common genes between IBD and NASH were extracted and imported to STRING database to construct PPI network. The resulting network contained 99 nodes and 333 edges. Five genes were selected as hubs: JAK2, TLR2, TP53, TLR4 and STAT3 and five genes were selected as bottleneck including: JAK2, TP53, AGT, CYP3A4 and TLR4. These genes were hubs in analysis network that was constructed from hubs of NASH and IBD networks.
Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers.
Keywords: In?ammatory bowel diseases (IBD), Non-alcoholic steatohepatitis (NASH), Protein-protein interaction (PPI) network analysis, Hub-bottlenecks, Protein clusters.
- In?ammatory bowel diseases (IBD)
- Non-alcoholic steatohepatitis (NASH)
- Protein-protein interaction (PPI) network analysis
- Protein clusters
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