Fig 2. Deletion of the gene coding TRAM0076 changes the transcriptome of Methanococcus maripaludis . ( A ) A volcano diagram shows the distribution of 961 differentially expressed genes (DEG) in the Δ 0076 mutant. Red and green dots refer to 495 up- and 466 down-regulated genes, respectively. The dashed line denotes the thresholds for defining the differential expression by an adjusted P value Padj < 0.05, which was determined by a DESeq algorithm as described in Methods. Arrows identify genes that were upregulated in the Δ 0076 mutant and encode proteins interacting RNAs. ( B ) Hierarchical clustering for the differentially-expressed genes in triplicate cultures of the Δ 0076 mutant. The heat plot representation of the log2 of differential expression fold change is shown with color intensity, by red and blue representing the maxima and minima abundance, respectively. ( C ) The functional category enrichment ratio was calculated as the gene numbers of up- or down-regulated genes divided by the total numbers of genes in each functional category, and the top 10 and 12 mostly enriched up- and down-regulated gene categories were shown respectively. The enrichment intensity (%) (red box) and the gene numbers that account for the up (orange)- or down (green)-regulated genes in the listed enriched category were also shown.