# A Special Structural Based Weighted Network Approach for the Analysis of Protein Complexes
## 5 Results and Discussion
### Function Enrichment Analysis
In addition, in Table A5, we see that WECALM detected a large number of complexes with a 100% cluster frequency. In the detection of protein complexes, a cluster frequency of 100% means that a particular complex is detected in all runs of the test. This is regarded as a very good indication of the findings' robustness and repeatability, as it implies that the complex is consistently detected by the algorithm across numerous replicates of the same experiment. WECALM had a very low \(p<10^{-10}\), indicating that the detected protein \begin{table}
\begin{tabular}{l l l l l l l l} \hline \hline
**Dataset** & **Algorithm** & \(\mathbf{C_{P}(v)}\) & \(\mathbf{p\leq 10^{-15}}\) & \(\mathbf{p\leq 10^{-10}}\) & \(\mathbf{p\leq 10^{-5}}\) & \(\mathbf{p\leq 10^{-2}}\) &
\begin{tabular}{l} **Significant** \\ **Detected \(\mathbf{C_{P}(v)}\)** \\ \end{tabular} \\ \hline BioGRID & MCL & 121 & 41 (33.88\%) & 28 (23.14\%) & 26 (21.49\%) & 12 (9.92\%) & 107 (88.43\%) \\  & COACH & 166 & 76 (45.78\%) & 32 (19.28\%) & 37 (22.29\%) & 16 (9.64\%) & 161 (96.98\%) \\  & EWCA & 1388 & 658 (47.41\%) & 211 (15.20\%) & 299 (21.54\%) & 173 (12.46\%) & 1341 (96.61\%) \\  & CFinder & 352 & 103 (29.26\%) & 53 (15.10\%) & 78 (22.16\%) & 35 (9.94\%) & 269 (76.42\%) \\  & GMFTP & 597 & 73 (12.23\%) & 59 (9.88\%) & 156 (26.13\%) & 161 (26.97\%) & 449 (75.21\%) \\  & Core & 576 & 255 (44.27\%) & 105 (18.23\%) & 68 (11.81\%) & 35 (6.08\%) & 463 (80.38\%) \\  & CALM & 1108 & 587 (52.98\%) & 236 (21.29\%) & 116 (10.47\%) & 96 (8.66\%) & 1035 (93.41\%) \\  & ClusterONE & 294 & 107 (36.40\%) & 35 (11.91\%) & 43 (14.62\%) & 25 (8.50\%) & 210 (71.43\%) \\  & CMC & 1113 & 125 (11.23\%) & 89 (7.99\%) & 258 (23.18\%) & 360 (32.34\%) & 832 (74.75\%) \\  & ProRank+ & 746 & 479 (64.21\%) & 105 (14.08\%) & 97 (13.00\%) & 47 (6.30\%) & 728 (97.59\%) \\  & WECALM & 1412 & 687 (48.65\%) & 217 (15.37\%) & 312 (22.09\%) & 172 (12.18\%) & 1388 (98.30\%) \\ \hline DIP & MCL & 142 & 41 (28.87\%) & 29 (20.42\%) & 17 (11.97\%) & 26 (18.31\%) & 113 (79.58\%) \\  & COACH & 329 & 21 (63.38\%) & 25 (7.59\%) & 66 (20.06\%) & 32 (9.73\%) & 144 (43.77\%) \\  & EWCA & 964 & 188 (19.50\%) & 126 (13.07\%) & 319 (33.09\%) & 236 (24.48\%) & 869 (09.15\%) \\  & CFinder & 352 & 157 (44.60\%) & 39 (11.08\%) & 31 (8.81\%) & 45 (12.78\%) & 272 (77.27\%) \\  & GMFTP & 548 & 43 (7.85\%) & 36 (6.57\%) & 105 (19.16\%) & 166 (30.29\%) & 350 (63.87\%) \\  & Core & 412 & 131 (31.79\%) & 87 (21.12\%) & 52 (12.62\%) & 45 (10.922\%) & 315 (76.46\%) \\  & CALM & 755 & 256 (33.91\%) & 127 (16.82\%) & 112 (14.83\%) & 108 (14.31\%) & 603 (80.53\%) \\  & ClusterONE & 315 & 119 (37.78\%) & 49 (15.56\%) & 38 (12.06\%) & 29 (9.21\%) & 235 (74.60\%) \\  & CMC & 303 & 3 (09.99\%) & 8 (2.64\%) & 58 (19.14\%) & 77 (25.41\%) & 146 (48.18\%) \\  & ProRank+ & 338 & 74 (21.89\%) & 77 (22.78\%) & 125 (36.98\%) & 41 (12.13\%) & 319 (93.79\%) \\  & WECALM & 1018 & 269 (26.42\%) & 187 (18.37\%) & 358 (35.17\%) & 165 (16.21\%) & 979 (96.17\%) \\ \hline \hline \end{tabular}
\end{table} 
Table 4: A function enrichment analysis of protein complexes detected on BioGRID and DIP complexes. complexes were biologically significant and meaningful and that they were most likely the true protein complexes, this can be used as a valuable benchmark in future research.