Name
Abstract | ||
|---|---|---|
The identification of protein complexes in protein-protein interaction (PPI) networks is fundamental for understanding biological processes and cellular molecular mechanisms. Many graph computational algorithms have been proposed to identify protein complexes from PPI networks by detecting densely connected groups of proteins. These algorithms assess the density of subgraphs through evaluation of the sum of individual edges or nodes; thus, incomplete and inaccurate measures may miss meaningful biological protein complexes with functional significance. In this study, we propose a novel method for assessing the compactness of local subnetworks by measuring the number of three node cliques. The present method detects each optimal cluster by growing a seed and maximizing the compactness function. To demonstrate the efficacy of the new proposed method, we evaluate its performance using five PPI networks on three reference sets of yeast protein complexes with five different measurements and compare the performance of the proposed method with four state-of-the-art methods. The results show that the protein complexes generated by the proposed method are of better quality than those generated by four classic methods. Therefore, the new proposed method is effective and useful for detecting protein complexes in protein-protein interaction networks. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1109/TCBB.2014.2386314 | IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) |
Keywords | Field | DocType |
data processing,protein complexes,protein-protein interaction networks,three node cliques,computational biology,clustering algorithms,bioinformatics,proteins,tin | Protein protein interaction network,Graph,Data processing,Computer science,Compact space,Theoretical computer science,Artificial intelligence,Bioinformatics,Cluster analysis,Machine learning | Journal |
Volume | Issue | ISSN |
PP | 99 | 1545-5963 |
Citations | PageRank | References |
4 | 0.40 | 16 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zhang Wei | 1 | 392 | 53.03 |
| Xiufen Zou | 2 | 272 | 25.44 |