PFC: An Efficient Soft Graph Clustering Method for PPI Networks Based on Purifying and Filtering the Coupling Matrix

2016 ◽  
pp. 247-257
Author(s):  
Ying Liu ◽  
Amir Foroushani
Keyword(s):  
Graph Clustering ◽  
Clustering Method ◽  
Coupling Matrix ◽  
Ppi Networks

scholarly journals Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins

Entropy ◽  
2021 ◽  
Vol 23 (10) ◽  
pp. 1271
Author(s):  
Hoyeon Jeong ◽  
Yoonbee Kim ◽  
Yi-Sue Jung ◽  
Dae Ryong Kang ◽  
Young-Rae Cho
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Clustering Algorithms ◽  
Graph Clustering ◽  
Functional Modules ◽  
Protein Protein Interactions ◽  
Overlapping Clusters ◽  
Novel Proteins ◽  
Ppi Networks ◽  
Function Modules

Functional modules can be predicted using genome-wide protein–protein interactions (PPIs) from a systematic perspective. Various graph clustering algorithms have been applied to PPI networks for this task. In particular, the detection of overlapping clusters is necessary because a protein is involved in multiple functions under different conditions. graph entropy (GE) is a novel metric to assess the quality of clusters in a large, complex network. In this study, the unweighted and weighted GE algorithm is evaluated to prove the validity of predicting function modules. To measure clustering accuracy, the clustering results are compared to protein complexes and Gene Ontology (GO) annotations as references. We demonstrate that the GE algorithm is more accurate in overlapping clusters than the other competitive methods. Moreover, we confirm the biological feasibility of the proteins that occur most frequently in the set of identified clusters. Finally, novel proteins for the additional annotation of GO terms are revealed.

scholarly journals A graph clustering method for community detection in complex networks

2017 ◽  
Vol 469 ◽  
pp. 551-562 ◽  
Author(s):  
HongFang Zhou ◽  
Jin Li ◽  
JunHuai Li ◽  
FaCun Zhang ◽  
YingAn Cui
Keyword(s):  
Complex Networks ◽  
Community Detection ◽  
Graph Clustering ◽  
Clustering Method

scholarly journals An Effective Graph Clustering Method to Identify Cancer Driver Modules

2020 ◽  
Vol 8 ◽  
Author(s):  
Wei Zhang ◽  
Yifu Zeng ◽  
Lei Wang ◽  
Yue Liu ◽  
Yi-nan Cheng
Keyword(s):  
Graph Clustering ◽  
Clustering Method ◽  
Cancer Driver

scholarly journals I-Louvain: An Attributed Graph Clustering Method

2015 ◽  
pp. 181-192 ◽  
Author(s):  
David Combe ◽  
Christine Largeron ◽  
Mathias Géry ◽  
Előd Egyed-Zsigmond
Keyword(s):  
Graph Clustering ◽  
Clustering Method ◽  
Attributed Graph

scholarly journals A METHOD FOR CONSTRUCTING DMAs BY A GRAPH CLUSTERING METHOD AND GENETIC ALGORITHMS

2015 ◽  
Vol 71 (4) ◽  
pp. 134-142
Author(s):  
Kenji KOIZUMI ◽  
Shingo ADACHI ◽  
Shinsuke TAKAHASHI ◽  
Takeshi TAKEMOTO ◽  
Hideyuki TADOKORO
Keyword(s):  
Genetic Algorithms ◽  
Graph Clustering ◽  
Clustering Method
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