scholarly journals Corrigendum: Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient

2021 ◽  
Vol 12 ◽  
Author(s):  
Yan Wang ◽  
Qiong Chen ◽  
Lili Yang ◽  
Sen Yang ◽  
Kai He ◽  
...  
Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2633 ◽  
Author(s):  
Fang Zhang ◽  
Anjun Ma ◽  
Zhao Wang ◽  
Qin Ma ◽  
Bingqiang Liu ◽  
...  

Overlapping structures of protein–protein interaction networks are very prevalent in different biological processes, which reflect the sharing mechanism to common functional components. The overlapping community detection (OCD) algorithm based on central node selection (CNS) is a traditional and acceptable algorithm for OCD in networks. The main content of CNS is the central node selection and the clustering procedure. However, the original CNS does not consider the influence among the nodes and the importance of the division of the edges in networks. In this paper, an OCD algorithm based on a central edge selection (CES) algorithm for detection of overlapping communities of protein–protein interaction (PPI) networks is proposed. Different from the traditional CNS algorithms for OCD, the proposed algorithm uses community magnetic interference (CMI) to obtain more reasonable central edges in the process of CES, and employs a new distance between the non-central edge and the set of the central edges to divide the non-central edge into the correct cluster during the clustering procedure. In addition, the proposed CES improves the strategy of overlapping nodes pruning (ONP) to make the division more precisely. The experimental results on three benchmark networks and three biological PPI networks of Mus. musculus, Escherichia coli, and Cerevisiae show that the CES algorithm performs well.


2005 ◽  
Vol 08 (04) ◽  
pp. 383-397 ◽  
Author(s):  
PO-HAN LEE ◽  
CHIEN-HUNG HUANG ◽  
JYWE-FEI FANG ◽  
HSIANG-CHUAN LIU ◽  
KA-LOK NG

We employ the random graph theory approach to analyze the protein–protein interaction database DIP. Several global topological parameters are used to characterize the protein–protein interaction networks (PINs) for seven organisms. We find that the seven PINs are well approximated by the scale-free networks, that is, the node degree cumulative distribution P cum (k) scales with the node degree k (P cum (k) ~ k-α). We also find that the logarithm of the average clustering coefficient C ave (k) scales with k (C ave (k) ~ k-β), for E. coli and S. cerevisiae. In particular, we determine that the E. coli and the S. cerevisiae PINs are better represented by the stochastic and deterministic hierarchical network models, respectively. The current fruit fly protein–protein interaction dataset does not have convincing evidence in favor of the hierarchical network model. These findings lead us to conclude that, in contrast to scale-free structure, hierarchical structure model applies for certain species' PINs only. We also demonstrate that PINs are robust when subject to random perturbation where up to 50% of the nodes are rewired. Average node degree correlation study supports the fact that nodes of low connectivity are correlated, whereas nodes of high connectivity are not directly linked.


Sign in / Sign up

Export Citation Format

Share Document