Attribute clustering for grouping, selection, and classification of gene expression data

• Published in: IEEE/ACM transactions on computational biology and bioinformatics 2005-04, Vol.2 (2), p.83-101
• Main Authors: Wai-Ho Au, Chan, K.C.C., Wong, A.K.C., Yang Wang
• Format: Article
• Language: English
• Subjects: Algorithms; attribute clustering; Bioinformatics; Cluster Analysis; Clustering algorithms; Clustering methods; Data analysis; Data mining; Databases, Protein; Gene expression; gene expression classification; Gene Expression Profiling - methods; gene selection; Gold; Information Storage and Retrieval - methods; microarray analysis; Multigene Family - physiology; Oligonucleotide Array Sequence Analysis - methods; Optimization methods; Partitioning algorithms; Pattern Recognition, Automated - methods
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2005.17

This paper presents an attribute clustering method which is able to group genes based on their interdependence so as to mine meaningful patterns from the gene expression data. It can be used for gene grouping, selection, and classification. The partitioning of a relational table into attribute subgroups allows a small number of attributes within or across the groups to be selected for analysis. By clustering attributes, the search dimension of a data mining algorithm is reduced. The reduction of search dimension is especially important to data mining in gene expression data because such data typically consist of a huge number of genes (attributes) and a small number of gene expression profiles (tuples). Most data mining algorithms are typically developed and optimized to scale to the number of tuples instead of the number of attributes. The situation becomes even worse when the number of attributes overwhelms the number of tuples, in which case, the likelihood of reporting patterns that are actually irrelevant due to chances becomes rather high. It is for the aforementioned reasons that gene grouping and selection are important preprocessing steps for many data mining algorithms to be effective when applied to gene expression data. This paper defines the problem of attribute clustering and introduces a methodology to solving it. Our proposed method groups interdependent attributes into clusters by optimizing a criterion function derived from an information measure that reflects the interdependence between attributes. By applying our algorithm to gene expression data, meaningful clusters of genes are discovered. The grouping of genes based on attribute interdependence within group helps to capture different aspects of gene association patterns in each group. Significant genes selected from each group then contain useful information for gene expression classification and identification. To evaluate the performance of the proposed approach, we applied it to two well-known gene expression data sets and compared our results with those obtained by other methods. Our experiments show that the proposed method is able to find the meaningful clusters of genes. By selecting a subset of genes which have high multiple-interdependence with others within clusters, significant classification information can be obtained. Thus, a small pool of selected genes can be used to build classifiers with very high classification rate. From the pool, gene expressions of different cat