Figure 1.
Pearson correlation coefficient between expression values of pairs of genes.
A) The genome-wide gene expression correlations of all the gene pairs and B) expression correlation between operonic gene pairs and randomly paired non-operonic gene pairs. As anticipated, it is evident that the genes on operons exhibit higher correlation in their expression compared to the non-operonic gene pairs.
Figure 2.
Plots indicating the distinctive behavior of the positive and negative protein interaction pairs with respect to genome context methods and gene expression correlations.
All the four features show statistically significant and distinct distribution for the positive and negative pairs. A) Phylogenetic Profile, B) Gene Distance, C) Operonic Method and D) Expression Correlation.
Table 1.
Topological Properties of the predicted protein functional linkages.
Figure 3.
Average clustering coefficient and degree of the proteins across metabolic pathways.
Proteins show high degree or high clustering coefficient depending on their function. Translation pathway proteins have high degree as well as high clustering coefficient whereas membrane transport proteins are highly clustered with less connectivity.
Figure 4.
Proportion of Essential Genes in the bins of decreasing centrality values.
For all the three centrality values calculated, namely degree, closeness and betweenness, it is clearly seen that there exists a good correlation between centrality and lethality.
Figure 5.
Expression Correlation between up and downregulated genes.
Upregulated genes correlate in their expression and a similar trend is observed for downregulated genes. However, there is inverse correlation in expression between up and downregulated genes.
Figure 6.
Graphical representation of functional interactions and regulatory interactions of up and downregulated genes.
DosR acts as a master regulator, regulating the expression of a number of upregulated genes. A probable oxidoreductase Rv0082 under the regulation of DosR associates with the subunits of aerobic respiratory machine NADH oxidoreductase complex. Upregulated proteins are colored in green, downregulated proteins are colored in red and transcription factors are colored in blue. Directed edge denotes gene regulation and undirected edge is a protein functional linkage.
Figure 7.
Schematic representation of the up and down-regulated modules.
Node color represents the class as follows: Green – Upregulated proteins; Red – Downregulated proteins; Purple – First neighbors of the upregulated proteins; Yellow – First neighbors of the downregulated proteins; Blue – Proteins interacting with both upregulated and downregulated proteins.
Figure 8.
A sub-network depicting the connectivity mediated by proteins Rv2621c and SseC2.
Both these proteins occur most frequently in the paths between up and downregulated genes. The upregulated proteins associating with Rv2621c are colored in green and the downregulated proteins associating with SseC2 are colored in red.