a temporal precedence based clustering method for gene expression microarray data基于时间优先的微阵列基因表达数据的聚类方法.pdfVIP

Krishna et al. BMC Bioinformatics 2010, 11:68 /1471-2105/11/68 RESEARCH ARTICLE Open Access A temporal precedence based clustering method for gene expression microarray data 1 1* 2 Ritesh Krishna , Chang-Tsun Li , Vicky Buchanan-Wollaston Abstract Background: Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of clustering techniques are based on distance or visual similarity measures which may not be suitable for clustering of temporal microarray data where the sequential nature of time is important. We present a Granger causality based technique to cluster temporal microarray gene expression data, which measures the interdependence between two time-series by statistically testing if one time-series can be used for forecasting the other time-series or not. Results: A gene-association matrix is constructed by testing temporal relationships between pairs of genes using the Granger causality test. The association matrix is further analyzed using a graph-theoretic technique to detect highly connected components representing interesting biological modules. We test our approach on synthesized datasets and real biological datasets obtained for Arabidopsis thaliana. We show the effectiveness of our approach by analyzing the results using the existing biological literature. We also report interesting structural properties of the association network commonly desired in any biological system. Conclusions: Our experiments on synthesized and real microarray datasets show that our approach produces encouraging results. The metho