Supplementary material

Protein Complex Prediction with RNSC

Andrew D. King, Natasha Przulj, Igor Jurisica

In "Bacterial Molecular Networks", Series: Methods in Molecular Biology, Eds. van Helden, Toussaint, Thieffry, The Humana Press Inc, Tatowa, NJ.

 

Restricted Neighbourhood Search Clustering Algorithm

FIGURE 1

Eight dense putative complexes identified by RNSC in the yeast protein interaction data. RNSC was run on the I2D yeast interaction database ver. 1.71 (http://ophid.utoronto.ca/i2d), a network of 6,027 proteins and 120,974 interactions (17, 18).  Of the 1, 276 multi-protein complexes output by RNSC, 702 had density at least 0.8, 93 had size at least nine, and 36 satisfied both criteria.  This figure shows the first eight of these 36 predicted complexes and the interactions between all member vertices.  The largest consists of 40 proteins and has density 0.84. For simplicity, individual complexes and interactions within them are highlighted with different colour for nodes and edges. The network was visualized using NAViGaTOR 2.1.14 (http://ophid.utoronto.ca/navigator) (16).

FIGURE 2

Five dense putative complexes identified by RNSC in the E.coli protein interaction data from (20). RNSC was run on a network with 2,283 proteins and 7,613 interactions. Five large and dense putative complexes have been identified: Cluster #0 with 16 nodes, density 0.675000; Cluster #1 with 15 nodes, density 0.590476; Cluster #2 with 15 nodes, density 0.780952; Cluster #3 with 15 nodes, density 0.733333; Cluster #4 with 51 nodes, density 0.520784; Cluster #5 with 15 nodes, density 0.523810. Two of the putative complexes are further interconnected (shown with dashed edges). Clusters #2 and #4 are linked by 41 edges between 27 proteins, and clusters #2 and #5 are linked by 2 edges between 3 proteins. For simplicity, individual putative complexes and interactions within them are highlighted with different colour for nodes and edges, and other nodes and edges are kept partially transparent. The network was visualized using NAViGaTOR 2.1.14 (http://ophid.utoronto.ca/navigator) (16).