A novel noise handling method to improve clustering of gene expression patterns
© Bhattacharya and De; licensee BioMed Central Ltd. 2011
Published: 5 August 2011
Cluster analysis of gene expression data is a useful tool for identifying biologically relevant groups of genes that show similar expression patterns under multiple experimental conditions. Performance of clustering algorithms is largely dependent on selected similarity measure. Efficiency in handling outliers is a major contributor to the success of a similarity measure. In gene expression data, there may be pairs of genes that have completely different expression values over a few samples under certain experimental condition(s), although they exhibit similar behavior over the other samples. Depending on the algorithms, these outliers are either placed in single element clusters (hierarchical clustering), are allowed to be in a cluster that is more similar compared to others (partitioning clustering) or they may be completely discarded from grouping (density-based, grid-based and graph-based clustering). In all these cases outliers affect the outcome of a clustering result. Measurement errors or conditional changes during microarray experiments may cause a single sample, if not more, differing in expression level to a great extent compared to the other samples. Expression value of the single or a very few outlier samples may cause a gene to be an outlier. We formulate a new weighted function based method to reduce the effect of outliers on similarity measures. The better the similarity measure is in measuring similarity between genes in the presence of outliers, the better the performance of the clustering algorithm will be in forming biologically relevant groups of genes.
- Jain AK, Dubes RC: Algorithms for Clustering Data. New Jersey: Prentice Hall; 1988.Google Scholar
- Bansal N, Blum A, Chawla S: Correlation clustering. Machine Learning 2004, 56: 89–113. 10.1023/B:MACH.0000033116.57574.95View ArticleGoogle Scholar
- Bhattacharya A, De RK: Divisive correlation clustering algorithm (DCCA) for grouping of genes: Detecting varying patterns in expression profiles. Bioinformatics 2008, 24: 1359–1366. 10.1093/bioinformatics/btn133View ArticlePubMedGoogle Scholar
- Bhattacharya A, De RK: Average correlation clustering algorithm (ACCA) for grouping of co-regulated genes with similar pattern of variation in their expression values. Journal of Biomedical Informatics 2010, 43: 560–568. 10.1016/j.jbi.2010.02.001View ArticlePubMedGoogle Scholar
- Bhattacharya A, De RK: Bi-correlation clustering algorithm for determining a set of co-regulated genes. Bioinformatics 2009, 25: 2795–2801. 10.1093/bioinformatics/btp526View ArticlePubMedGoogle Scholar
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