NDLI: Clustering Microarray Data by Using a Stochastic Algorithm

Content Provider	IEEE Xplore Digital Library
Author	Ho Sun Shon Sunshin Kim Seung Jung Shin Keun Ho Ryu
Copyright Year	2008
Description	Author affiliation: Database/Bioinf. Lab., Chungbuk Nat. Univ., Cheongju (Ho Sun Shon)
Abstract	The clustering of gene expression data is used to analyze the results of microarray studies. This method is often useful in understanding how a particular class of genes functions together during a biological process. In this study, we attempted to perform clustering using the Markov cluster (MCL) algorithm, a clustering method for graphs based on the simulation of stochastic flow. It is a fast and efficient algorithm that clusters nodes in a graph through simulation by computing probability. First, we converted the raw matrix into a sample matrix using the Euclidean distance of the genes between the samples. Second, we applied the MCL algorithm to the new matrix of Euclidean distance and considered 2 factors, namely, the inflation and diagonal terms of the matrix. We have turned to set the proper factors through massive experiments. In addition, distance thresholds, i.e., the average of each column data elements, were used to clearly distinguish between groups. Our experimental result shows about 70% accuracy in average compared to the class that is known before. We also compared the MCL algorithm with the self-organizing map (SOM) clustering, K-means clustering and hierarchical clustering (HC) algorithms.
Starting Page	456
Ending Page	461
File Size	163159
Page Count	6
File Format	PDF
ISBN	9780769532424
DOI	10.1109/CIT.2008.Workshops.117
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-07-08
Publisher Place	Australia
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	K-means Biological system modeling Computational modeling Clustering methods Stochastic processes Gene expression Microarray MCL algorithm SOM Clustering algorithms Biological processes Euclidean distance Biology computing hierarchical clustering Matrix converters
Content Type	Text
Resource Type	Article

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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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