Clustering protein-protein interaction network of TP53 tumor suppressor protein using Markov clustering algorithm

Thia Sabel Permata, Alhadi B.

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

17 Citations (Scopus)

Abstract

The formation and proliferation of tumor cells occurs if a special protein that regulates cell division experience any changing on their function, gene expression or both of them. One of the tumor suppressor proteins that plays a significant role in controlling the cell cycle is the TP53 protein. In most of the genetic changes in the tumor, it found that mutant of TP53 is a high risk factor for cancer. Therefore, it is important to conduct studies on clustering protein-protein interactions (PPI) network of TP53. PPI networks are generally presented in the graph network with proteins as vertices and interactions as edges. Markov clustering (MCL) algorithm is a graph clustering method which based on a simulation of stochastic flow on a graph. In implementation, we applied MCL process using the Python programming language. The clustering datasets are the PPI of TP53 obtained from the STRING database. MCL algorithm consists of three main operations such as expansion, inflation, and prune. We conduct the clustering simulation using different parameter of expansion, inflation and the multiplier factor of identity matrix. As the results we found the MCL algorithm is proven to produce robust cluster with TP53 protein as a centroid for each clustering results.

Original languageEnglish
Title of host publicationICACSIS 2015 - 2015 International Conference on Advanced Computer Science and Information Systems, Proceedings
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages221-226
Number of pages6
ISBN (Electronic)9781509003624
DOIs
Publication statusPublished - 19 Feb 2016
EventInternational Conference on Advanced Computer Science and Information Systems, ICACSIS 2015 - Depok, Indonesia
Duration: 10 Oct 201511 Oct 2015

Publication series

NameICACSIS 2015 - 2015 International Conference on Advanced Computer Science and Information Systems, Proceedings

Conference

ConferenceInternational Conference on Advanced Computer Science and Information Systems, ICACSIS 2015
Country/TerritoryIndonesia
CityDepok
Period10/10/1511/10/15

Keywords

  • Centroid
  • Markov clustering (MCL)
  • TP53 Protein
  • Tumor Cell
  • protein-protein interaction (PPI) network

Fingerprint

Dive into the research topics of 'Clustering protein-protein interaction network of TP53 tumor suppressor protein using Markov clustering algorithm'. Together they form a unique fingerprint.

Cite this