Identification of gene expression patterns using planned linear contrasts

Background: In gene networks, the timing of significant changes in the expression level of each gene may be the most critical information in time course expression profiles. With the same timing of the initial change, genes which share similar patterns of expression for any number of sampling intervals from the beginning should be considered co-expressed at certain level(s) in the gene networks. In addition, multiple testing problems are complicated in experiments with multi-level treatments when thousands of genes are involved. Results: To address these issues, we first performed an ANOVA F test to identify significantly regulated genes. The Benjamini and Hochberg (BH) procedure of controlling false discovery rate (FDR) at 5% was applied to the P values of the F test. We then categorized the genes with a significant F test into 4 classes based on the timing of their initial responses by sequentially testing a complete set of orthogonal contrasts, the reverse Helmert series. For genes...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Hao Li, Constance L. Wood, Yushu Liu, Thomas V. Getchell, Marilyn L. Getchell, Arnold J. Stromberg
• Keywords: BMCBI 2006, Gene, Gene Networks, Subsequent Sampling Time