Fig. 3
From: EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data
EPIG-Seq analysis of the toxicogenomics MOA data. a Thumbnail plots of the gene expression profiles that are the representatives (those with the highest PCS) of each of the extracted patterns from the toxicogenomics MOA data. The title of each thumbnail plot indicates the number of the pattern extracted and the gene symbol. MOA groups are color-coded as follows: Control (green), AhR 2 (red), CAR/PXR (yellow), Cytotox (light blue), DNA Damage (blue) and PPARA (pink), with 9 samples (groups of 3 biological replicates per chemical) in each. The y-axis is the log base 2 ratio of each sample data RPM relative to the average of the control. b The heat map representation of the genes clustered to the four extracted patterns from the EPIG-Seq analysis of the toxicogenomics MOA data. The symbols of the genes are shown to the left of the heat map with the 4 colors indicative of the pattern number assigned to. The columns indicate the chemicals within each of the MOA groups. The color scale represents the log base 2 ratio of each sample data relative to the average of the control. c PCA of the toxicogenomics MOA data using the CYs correlation measures of the genes clustered to the patterns by EPIG-Seq. The groups are color-coded as denoted in the legend. The x-axis is PC1, the y-axis is PC2 and the z-axis is PC3