Fig. 6

A 27 × 27 Comparative Pattern Count (COMPACT) matrix representing pair-wise counts of differential gene expression patterns comparing Ethanol and Carbohydrate groups. First, the differential gene expression at each time point was computed relative to appropriate, likely time point specific, control conditions. The time series data was averaged across replicates within each sample group, and discretized into up-(red), down-(green), and no-regulation (white) based on a threshold (1.5) of differential expression level. The sample groups were divided into two sets based on the comparative pair: Disease versus Normal. Within each set, the discretized time series expression data was collated for each gene into a pattern vector. Pairs of diet groups were compared to count the number of genes that follow each of the 27 * 27 (=729) possibilities to create a 27 × 27 matrix representing the comparative dynamic response pattern counts. The elements of the COMPACT matrix are based on pair-wise gene counts of the corresponding patterns, i.e., the element at the i^th row and j^th column of the matrix contains the number of genes that show an i^th expression pattern in Carbohydrate group and j^th expression pattern in Ethanol group. The diagonal of the matrix (yellow) represents those genes showing a common response and the off-diagonal elements of the 27 × 27 matrix represent the genes showing an altered temporal response between the two comparative conditions. The matrix was partitioned such that the pattern representing no differential regulation at 1 h broadly separates the up-and downregulation in the early response to PHx at 1 h. This yielded 9 sections corresponding to pair-wise combinations based on differential regulation at 1 h. The dominant patterns in section e reveal that the majority of the gene expression response occurred at 6 h and 24 h, but not at 1 h post PHx. The difference in gene counts in this section is highlighted using white (smallest) to dark brown (largest) set. Sections c and g corresponding to opposite regulation at 1 h between the dietary groups were nearly empty. Sections b, d, f and h correspond to genes that showed 1 h response only in one of the dietary groups. Sections a and i correspond to similar direction of regulation at 1 h, with the off-diagonal counts in these sections corresponding to genes with ethanol-altered patterns of regulation at 6 h and 24 h. Section e can also be subdivided based on differential regulation at 6 h, and showed similarities in overall structure, for example, with the largely empty anti-diagonal subsections (c and g) corresponding to opposite regulation at 6 h