Figure 6: Identifying dense sub-graphs
An E. coli protein-protein interaction network comprising 106 proteins and 1,529 interactions representing the local interactome of Penicillin Binding Proteins 2, 3, 5, and 6A. Data generated from (60). RNSC predicted complexes in the E. coli PPI network from (60) are highlighted. The full network comprises 2,283 proteins and 7,613 interactions, giving it an overall interaction density of 2.9·10-3. Visualization was done in NAViGaTOR (ver. 12.1.14; http://ophid.utoronto.ca/navigator) (61).
Figure 6 data in NAViGaTOR XML format
Supplemental Figure 1: Identifying dense sub-graphs.
Using RNSC algorithm (62, 63), we clustered network from (64):Figure 2, and highlighted dense sub-graphs that are formed in the EGFR pathway network, generated from the 122 core f-EGFR proteins (i.e., proteins corresponding to the EGFR pathway genes identified to have functional SNPs). The triangular nodes represent the 122 core f-EGFR proteins and the 71 blue nodes represent those proteins in the ERBB pathway that are also members of this PPI network. The 26 blue triangle nodes are proteins that belong to both the core f-EGFR proteins and EGFR pathway. The 8 nodes framed in red are highly connected in this PPI network. Individual putative complexes are highlighted with thick edges, and cross-talk between them is visualized with thinner edges. All other proteins and interactions are partially translucent to simplify the network. Edge and node attributes are defined in legend. Visualization was done in NAViGaTOR (ver. 12.1.14; http://ophid.utoronto.ca/navigator) (61).
Supplemental Table 1: All motifs identified by FANMOD.
The complete list of size six motifs found in Figure 6, arranged according to Z-scores.
