Identification of the Disrupted Pathways Associated with Periodontitis Based on Human Pathway Network

• Published in: Infection international Vol. 5; no. 4; pp. 93 - 98
• Main Authors: Sun, Wen, Han, Lin, Xu, Wenmao, Sun, Yazhen
• Format: Journal Article
• Language: English
• Published: De Gruyter Open 01.12.2016
• Subjects: disrupted pathways; EB co-expression; periodontitis; protein-protein interactions
• ISSN: 2544-0349; 2544-0349
• DOI: 10.1515/ii-2017-0143

: The objective of this work is to search for a novel method to explore the disrupted pathways associated with periodontitis (PD) based on the network level. : Firstly, the differential expression genes (DEGs) between PD patients and cognitively normal subjects were inferred based on LIMMA package. Then, the protein-protein interactions (PPI) in each pathway were explored by Empirical Bayesian (EB) co-expression program. Specifically, we determined the 100th weight value as the threshold value of the disrupted pathways of PPI by constructing the randomly model and confirmed the weight value of each pathway. Meanwhile, we dissected the disrupted pathways under the weight value > the threshold value. Pathways enrichment analyses of DEGs were carried out based on Expression Analysis Systematic Explored (EASE) test. Finally, the better method was selected based on the more rich and significant obtained pathways by comparing the two methods. : After the calculation of LIMMA package, we estimated 524 DEGs in all. Then we determined 0.115222 as the threshold value of the disrupted pathways of PPI. When the weight value>0.115222, there were 258 disrupted pathways of PPI enriched in. Additionally, we observed those 524 DEGs that were enriched in 4 pathways under EASE=0.1. : We proposed a novel network method inferring the disrupted pathway for PD. The disrupted pathways might be underlying biomarkers for treatment associated with PD.