Figure 1.
The node and edge number against cutoff values for three methods.
For the CLR method, the cutoff value represents the Z-score with a minimal value of 3.34 corresponding to the 60% confidence level of the FDR test; for the PCC and SCC methods, the cutoff value represents the correlation coefficient. The minimal correlation coefficient is 0.6.
Figure 2.
Overall performance of three methods for four protein complexes.
The F-score against the cutoff values (X-axis) of three methods for each protein complex is presented. Blue, CLR method; Pink, PCC method; Green, SCC method. For the CLR method, the cutoff value means the different confidence levels of the FDR test; for the PCC and SCC methods, the cutoff values represent the correlation coefficient.
Table 1.
Detailed information of 21 modules containing more than 100 genes in the TGN.
Figure 3.
Possible components of the Tetrahymena proteasome complex.
A, KEGG annotated Tetrahymena proteasome complex (http://www.kegg.jp/kegg-bin/show_pathway?tet03050); B, Silver stained gel of a pull down experiment using Dss1 (Rpn15) as bait that identifies proteins of the Tetrahymena proteasome; C, The network of the possible Tetrahymena proteasome complex.
Figure 4.
The distribution of the gained partners number of genes in TGN.
The X-axis indicates the gained partners (each represents an edge) of genes, the value was Log2 transformed. The Y-axis indicates the frequency of gained partners number, also Log2 transformed.
Figure 5.
The heatmap of the 1200 hub genes in TGN.
The heatmap was clustered by Euclidean distance of expression. The levels of expression are illustrated by different grades of color as determined from microarray data indicated along the top (from left to right). The color scale is as follows: dark color, low expression; light color, high expression. Levels of expression were obtained for 20 points in time during three physiological/developmental stages of the life cycle of Tetrahymena: For growing cells, L-l, L-m and L-h correspond to ∼1×105 cells/ml, ∼3.5×105 cells/ml and ∼1×106 cells/ml, respectively. For measurements of expression during starvation, ∼2×105 cells/ml were collected at intervals of 0, 3, 6, 9, 12, 15 and 24 hours (referred to as S-0, S-3, S-6, S-9, S-12, S-15 and S-24, respectively). For measurements of expression during conjugation, equal volumes of B2086 and CU428 cells were mixed following 18 h of starvation, and samples were collected at intervals of 0, 2, 4, 6, 8, 10, 12, 14, 16 and 18 h after mixing (referred to as C-0, C-2, C-4, C-6, C-8, C-10, C-12, C-14, C-16 and C-18, respectively). The 1,200 genes were sorted into six groups according to clustering analysis.