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

Content Provider	IEEE Xplore Digital Library
Author	Permata, Thia Sabel Bustamam, Alhadi
Copyright Year	2015
Description	Author affiliation: Department of Mathematics, University of Indonesia, UI, Depok, Indonesia (Permata, Thia Sabel; Bustamam, Alhadi)
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.
Starting Page	221
Ending Page	226
File Size	803400
Page Count	6
File Format	PDF
e-ISBN	9781509003631
DOI	10.1109/ICACSIS.2015.7415177
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-10-10
Publisher Place	Indonesia
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Centroid Zirconium RNA Markov clustering (MCL) Clustering algorithms Random access memory TP53 Protein Protein-protein interaction (PPI) network Tumor Cell Bioinformatics Joining processes
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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