Name
Title | ||
|---|---|---|
Identification of Protein Complexes Using Weighted PageRank-Nibble Algorithm and Core-Attachment Structure |
Abstract | ||
|---|---|---|
Protein complexes play a significant role in understanding the underlying mechanism of most cellular functions. Recently, many researchers have explored computational methods to identify protein complexes from protein-protein interaction (PPI) networks. One group of researchers focus on detecting local dense subgraphs which correspond to protein complexes by considering local neighbors. The drawback of this kind of approach is that the global information of the networks is ignored. Some methods such as Markov Clustering algorithm (MCL), PageRank-Nibble are proposed to find protein complexes based on random walk technique which can exploit the global structure of networks. However, these methods ignore the inherent core-attachment structure of protein complexes and treat adjacent node equally. In this paper, we design a weighted PageRank-Nibble algorithm which assigns each adjacent node with different probability, and propose a novel method named WPNCA to detect protein complex from PPI networks by using weighted PageRank-Nibble algorithm and core-attachment structure. Firstly, WPNCA partitions the PPI networks into multiple dense clusters by using weighted PageRank-Nibble algorithm. Then the cores of these clusters are detected and the rest of proteins in the clusters will be selected as attachments to form the final predicted protein complexes. The experiments on yeast data show that WPNCA outperforms the existing methods in terms of both accuracy and p-value.The software for WPNCA is available at “http://netlab.csu.edu.cn/bioinfomatics/weipeng/WPNCA/download.html”. |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1109/TCBB.2014.2343954 | IEEE/ACM Trans. Comput. Biology Bioinform. |
Keywords | Field | DocType |
cellular functions,protein interaction network,pagerank-nibble algorithm,cellular biophysics,protein-protein interaction networks,random processes,ppi networks,random walk technique,markov clustering algorithm,proteins,computational methods,weighted pagerank-nibble algorithm,markov processes,core-attachment structure,molecular biophysics,wpnca,random walk,protein complex,local dense subgraphs,mcl,probability,computational biology,bioinformatics,vectors,clustering algorithms | Cluster (physics),Nibble,Global structure,Random walk,Computer science,Global information,Software,Artificial intelligence,Cluster analysis,PageRank,Algorithm,Bioinformatics,Machine learning | Journal |
Volume | Issue | ISSN |
12 | 1 | 1545-5963 |
Citations | PageRank | References |
15 | 0.58 | 19 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Wei Peng | 1 | 59 | 5.06 |
| Jianxin Wang | 2 | 2163 | 283.94 |
| Bihai Zhao | 3 | 24 | 3.74 |
| Lusheng Wang | 4 | 2433 | 224.97 |