Table 1.
Enzymes associated with the chitin metabolic pathway that satisfy the condition of being present in more than 100 organisms from the 1695 original data set, downloaded from GeneBank at May 19th, 2007.
Figure 1.
The size of the largest connected component (Nc) versus the threshold similarity σ: a) Acetyl; b) UDP.
Figure 2.
The distance δ(σ,σ+Δσ) between networks for successive similarities at the maximal value, with Δσ = 1, in the case of: a) Acetyl at σ = σmax = 42%; b) UDP at σ = σma = 51%.
Figure 3.
The dendrogram produced by the successive elimination of links with largest value of betweeness in the case of Acetyl: a) for σ = 30%<42%; b) for σ = σmax = 42% that reveals the modular structure of the network.
Figure 4.
The neighborhood matrix with the 11 modules for Acetyl at σ = σmax = 42%.
Figure 5.
The standard network representation of Acetyl at σ = σmax = 42% (using Pajek package) with the communities that were indicated in Figure 4.
We label as C12 the small sub-graphs and isolated nodes that do not constitute a biologically meaningful community.
Table 2.
Summary of the results for each of the five enzyme networks: values of σmax corresponding to the largest peaks in the graphs δ×σ; number of nodes; number of distinct organisms; and the number of distinct communities.
Table 3.
Values of congruence obtained after pair-wise comparison of the phylogenetic analysis provided by two different networks.
Figure 6.
Series of spikes representing the 382 organisms present in each one of the 5 selected enzymes associated with the chitin metabolic route.
Along each series of spikes, color identifies the group the organisms belong to. There is no color correspondence between two network classifications.
Table 4.
Values of congruence obtained after pair-wise comparison of the phylogenetic analysis based on chitin synthase sequences provided by five different methods: Bayesian (B), distance (D), likelihood (L), parsimony (P), and the network method introduced herein (N).