Volume 9 Number 5 (May 2014)
Home > Archive > 2014 > Volume 9 Number 5 (May 2014) >
JSW 2014 Vol.9(5): 1157-1162 ISSN: 1796-217X
doi: 10.4304/jsw.9.5.1157-1162

Function prediction of proteins in yeast networks based on the MCL algorithm

Ke Zhan1, 2, YunQuan Zhang1, 2, 3
1University of Chinese Academy of Sciences ,Beijing 100190, China
2Laboratory of Parallel Software and Computational Science, Institute of Software, Chinese Academy of Sciences, Beijing 100190, China
3State Key Lab. of Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China


Abstract—Large-scale Protein-Protein interaction data sets exist in Saccharomyces cerevisiae due to many interaction detection methods such as yeast two-hybrid assay, mass spectrometry of purified complexes, correlated mRNA expression profile and so on. How to make use of these data sets to understand the protein function is very important. We use the algorithm [17] developed by Stijn van Dongen to describe the functional modules in PPI networks.We analyze four protein-protein networks from Saccharomyces cerevisiae, and our results suggest that the functional modules detected are consistent with the biology knowledge. Protein- Protein interaction network was separated into clusters using MCL algorithm. Based on the clusters resulted from MCL algorithm, we assign the function annotations using Pvalue and majority methods. The majority method is based on the majority rule [15]. The predicted function of proteins provide clue to biology experiments. Two methods are used to assign function annotations for the known clusters and unknown proteins, we compare the two predicted results, the results show that the two methods are consistent with each other.

Index Terms—function prediction , protein-protein interaction, MCL algorithm

[PDF]

Cite: Ke Zhan, YunQuan Zhang, "Function prediction of proteins in yeast networks based on the MCL algorithm," Journal of Software vol. 9, no. 5, pp. 1157-1162, 2014.

General Information

ISSN: 1796-217X (Online)
Frequency:  Bimonthly (Since 2020)
Editor-in-Chief: Prof. Antanas Verikas
Executive Editor: Ms. Yoyo Y. Zhou
Abstracting/ Indexing: DBLP, EBSCO, Google Scholar, ProQuest, INSPEC(IET), ULRICH's Periodicals Directory, WorldCat, etc
E-mail: jsw@iap.org
  • Apr 26, 2021 News!

    Vol 14, No 4- Vol 14, No 12 has been indexed by IET-(Inspec)     [Click]

  • Jun 22, 2020 News!

    Papers published in JSW Vol 14, No 1- Vol 15 No 4 have been indexed by DBLP     [Click]

  • Sep 13, 2021 News!

    The papers published in Vol 16, No 6 have all received dois from Crossref    [Click]

  • Jan 28, 2021 News!

    [CFP] 2021 the annual meeting of JSW Editorial Board, ICCSM 2021, will be held in Rome, Italy, July 21-23, 2021   [Click]

  • Sep 13, 2021 News!

    Vol 16, No 6 has been published with online version     [Click]