Fig. 8

Differential expression summary. Selection of plots is reported by eUTOPIA for the differential expression analysis results. The UpSet plot (a) represents the intersection between the sets of differentially expressed genes from various comparisons/contrasts in the limma setup. The vertical bar plot reports the intersection size, the dot plot reports the set participation in the intersection, and the horizontal bar plot reports the set sizes. The volcano plot (b) represents the distribution of differentially expressed genes by log2(Fold Change) and -log10(P.value) as a scatter plot. The log2(Fold Change) values are plotted on the x-axis, the range of values is from the negative logFC to positive logFC with zero in the middle. The blue vertical margins on the plot represent the user specified logFC cutoff. The -log10(P.Value) values are plotted on the y-axis, the red horizontal margin represents the user specified P. Value cutoff. The plotted values outside the cutoff margins are colored red to highlight the significant differentially expressed features. The heatmap (c) represents the top differentially expressed features. The samples are reported in rows, and the features are reported in columns. The log-transformed expression values are represented by the color as per the ‘Color Key’. The clustering of samples based on the expression distribution of the reported features is presented on the top of the heatmap. The color blocks below the hierarchical cluster represent the sample group annotation