IMR Press / FBL / Volume 10 / Issue 3 / DOI: 10.2741/1763

Frontiers in Bioscience-Landmark (FBL) is published by IMR Press from Volume 26 Issue 5 (2021). Previous articles were published by another publisher on a subscription basis, and they are hosted by IMR Press on imrpress.com as a courtesy and upon agreement with Frontiers in Bioscience.

Open Access Article
Finding dominant sets in microarray data
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1 State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, PR China
2 Department of Computer Science and Engineering, Fudan University, Shanghai 200433, PR China
3 Department of Mathematics, Fudan University, Shanghai 200433, PR China
Front. Biosci. (Landmark Ed) 2005, 10(3), 3068–3077; https://doi.org/10.2741/1763
Published: 1 September 2005
Abstract

Clustering allows us to extract groups of genes that are tightly coexpressed from Microarray data. In this paper, a new method DSF_Clust is developed to find dominant sets (clusters). We have preformed DSF_Clust on several gene expression datasets and given the evaluation with some criteria. The results showed that this approach could cluster dominant sets of good quality compared to kmeans method. DSF_Clust deals with three issues that have bedeviled clustering, some dominant sets being statistically determined in a significance level, predefining cluster structure being not required, and the quality of a dominant set being ensured. We have also applied this approach to analyze published data of yeast cell cycle gene expression and found some biologically meaningful gene groups to be dug out. Furthermore, DSF_Clust is a potentially good tool to search for putative regulatory signals.

Keywords
Microarray data
dominant sets
cluster
correlation coefficient
significance level
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