Generalized estimating equations by considering additive terms for analyzing time-course gene sets data

Time-course gene sets are collections of predefined groups of genes in some patients gathered over time. The analysis of time-course gene sets for testing gene sets which vary significantly over time is an important context in genomic data analysis. In this paper, the method of generalized estimating equations (GEEs), which is a semi-parametric approach, is applied to time-course gene set data. We propose a special structure of working correlation matrix to handle the association among repeated measurements of each patient over time. Also, the proposed working correlation matrix permits estimation of the effects of the same gene among different patients. The proposed approach is applied to an HIV therapeutic vaccine trial (DALIA-1 trial). This data set has two phases: pre-ATI and post-ATI which depend on a vaccination period. Using multiple testing, the significant gene sets in the pre-ATI phase are detected and data on two randomly selected gene sets in the post-ATI phase are also analyzed. Some simulation studies are performed to illustrate the proposed approaches. The results of the simulation studies confirm the good performance of our proposed approach.