Fig. 4

Genes differentially expressed under distinct pH conditions. a Venn diagram shows the amount of differentially expressed genes, common or specific to the pairwise compared samples. b Heat map which indicates the correlation between transcriptional profiles across samples (Spearman correlation). In this case, the color scale indicates the degree of correlation between the treatments (pH 5.0, 6.0, and 7.0). Green and red represent a weak or strong correlation between the samples, respectively. c The expression profile of pH-responsive genes showing as a heat map after DEseq normalization and the hierarchical clustering analysis. TPM (transcripts per million) values in a log₂ scale were used. These values were independently calculated for each of the three biological replicates (R1, R2, and R3) performed for each of the three conditions (pH 5.0, 6.0, and 7.0, respectively). For coloring purposes, each row represents the expression of a single transcript (nr-unigenes) where shades of yellow represent high expression levels while the shades of purple represent low expression levels. In both heat maps, biological replicates are shown independently to show their reproducibility