Classification of KEGG pathways into essential-gene-enriched pathways (EEPs) and TATA-containing-gene-enriched pathways (TEPs).

<p>(a) We created a network to show which KEGG pathway (ellipse node) belongs to EEPs or TEPs (round rectangle nodes) and which one is included in metabolic pathways (diamond node in the center). The relations are described as edges between two nodes; for instance, glycolysis belongs to TEPs and metabolic pathways. Color (upper-right) represents an adjusted p-value in enrichment analysis. (b) The bar graph shows the results of GO (gene ontology) enrichment analysis in EEPs and TEPs. The red dashed lines correspond to the log transformation of an adjusted p-value of 0.05. BP, biological process; MF, molecular function.</p

Comparison of pathways in TEPs and EEPs on metabolic map.

<p>(a) TEPs and (b) EEPs are associated with different modules in the metabolic pathways analysis; these are highlighted in color (red for TEPs and blue for EEPs). Most of the TEPs in the metabolic pathways are associated with carbohydrate metabolism. Circles indicate compounds in the metabolic pathways.</p

Marked differences in genes and pathways between EEPs and TEPs.

<p>(a) The heat map of the adjusted p-values obtained from the enrichment test showed that EEPs are obviously different from TEPs. Rows represent genes and columns pathways (pathway ID); colors represent the negative log transformation of the adjusted p-values, showing the extent to which essential and TATA genes are enriched in the corresponding pathways. (b) Essential-gene-enriched pathways (EEPs) and (c) TATA-containing-gene-enriched pathways (TEPs). The enriched pathways were sorted according to the negative log of the adjusted p-value. The red dashed lines correspond to the log transformation of an adjusted p-value of 0.05.</p

Enrichment of metabolic pathways and enzyme.

<p>(a) There is a marked difference in the enriched metabolic pathways between TATA and essential genes. (b) Oxidoreductases are enriched in the enzyme set (197 enzymes) of the TEPs, whereas transferases are enriched in the enzyme set (124) of the EEPs. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05.</p

Degrees and connectivity in the interaction network.

<p>(a) The mean degrees of molecular interactions are significantly higher (p<0.05) in genes of EEPs than in genes of TEPs. (b) Genes of EEPs were over-represented for higher-scored or highly interconnected clusters, whereas those of TEPs were over-represented for less-scored clusters. The X-axis represents clusters that are displayed in the order of the scores, with the cluster in the left corner having the highest scores.</p

Functional comparison of EEPs and TEPs.

<p>(a) Genes of TEPs tend to be associated with a greater number of transcription factors than EEPs. (b) The transcription of TEPs is preferentially associated with the SAGA complex, a regulator of transcription that is known to be related to the stress response. The red dashed lines correspond to the negative log transformation of an adjusted p-value of 0.05. (c) Most TEPs exhibit a higher CAI (codon adaptation index) compared with the EEPs.</p