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Fig. 1 | BMC Genomics

Fig. 1

From: A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration

Fig. 1

A schematic representation of the comparative pattern count (COMPACT) analysis for multifactorial transcriptomic data. The approach considers an experimental design in which the transcriptomic effects of two conditions, termed “Comparative Pair”, (e.g., Disease versus Normal) are evaluated at multiple levels of another factor, termed “Pattern Set”, (e.g., time points, drug dose, weight group, cell type, etc.). The following explanation considers Disease versus Normal comparison at multiple time points, for illustration purposes. First, the differential gene expression at each time point is computed relative to appropriate, likely time point specific, control conditions. The time series data is averaged across replicates within each sample group, and discretized into up-, down-, and no-regulation based on a threshold of differential expression level. The sample groups are divided into two sets based on the comparative pair: Disease versus Normal. Within each set, the discretized time series expression data is collated for each gene into a pattern vector. The number of genes corresponding to each of the patterns within Disease or Normal sets provides a univariate distribution of patterns. The intersection between the Disease versus Normal pattern count distributions (i.e., the two-way histogram) exhaustively considers all possible comparative patterns, yielding a COMPACT matrix. The elements of the COMPACT matrix are based on pair-wise gene counts of the corresponding patterns, i.e., for the comparative pair Disease and Normal, the element at the ith row and jth column of the matrix contains the number of genes that show an ith expression pattern in Normal and jth expression pattern in Disease. The diagonal of the matrix represents those genes showing a common response and the off-diagonal elements represent the genes showing an altered temporal response between the two comparative conditions. The organization of the COMPACT matrix lends itself to a layered exploration of the genes with common, novel and altered differential expression patterns between the conditions in the Comparative Pair, as illustrated in the analysis below (e.g., Figs. 6 and 7). The COMPACT matrix, or subsets thereof, can be visualized using a chord diagram, providing additional means for layered exploration of the data, particularly when the matrix is relatively less sparse (e.g., as illustrated in Fig. 8)

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