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Table 3 Summary of topological and biological analysis of gene module and their corresponding protein modules for Set 1

From: Two-layer modular analysis of gene and protein networks in breast cancer

Module Id 1 2 3 4 5 6 7 #U Sum
Topological analysis         
Genes 142 142 125 40 35 22 7 513
Expressed proteins 640 486 439 159 152 79 10 1958
PPI 7465 6576 8163 2106 1317 885 126 24752
Processed protein in PPI 3284 3206 3187 1338 797 575 114 6519
Processed PPI 6951 6095 7712 1985 1250 794 113 23173
α 1.606 1.632 1.576 1.701 1.658 1.698 1.777  
Qmax 0.637 0.662 0.632 0.714 0.792 0.798 0.793  
Modules (Isolated modules) 309 (7) 259 (4) 28 (11) 26 (10) 23 (8) 17 (7) 6 (4) 155 (51)
%age accuracy, LOO-CV 86.510 87.410 95.199 99.028 99.624 100 100  
Avg. Qmax, LOO-CV 0.639 0.664 0.634 0.714 0.797 0.797 0.791  
Module range, LOO-CV 24-33 20-28 24-34 25-32 21-25 16-18 5-6  
Avg. Modules, LOO-CV 28 26 28 26 22 16 5  
Biological analysis         
GO:BP, Groups 137 135 111 71 45 34 6 539
GO:BP, Terms 96 117 96 67 47 37 8 205
GO:BP, Referenced 42 54 46 32 25 19 8 85
GO:MF, Groups 131 124 115 69 44 35 7 525
GO:MF, Terms 79 72 72 51 33 30 10 145
GO:MF, Referenced 55 40 43 34 24 23 8 91
GO:CC, Groups 112 95 92 55 42 32 6 434
GO:CC, Terms 15 14 14 11 10 13 6 23
GO:CC, Referenced 12 11 12 9 8 9 6 16
  1. Topological analysis represents the analysis of network topology, while biological analysis represents the domain analysis of individual modules; Genes, Number of genes; Expressed Proteins, Proteins expressed by genes in module; PPI, Number of interaction between proteins; Processed protein in PPI, Number of proteins after removing loops and multiple edges; Processed PPI, Number of interaction in processed PPI; α, Power law exponent; Qmax, maximum modularity score; LOO-CV, Leave-one-out cross-validation; Avg. modules, Mean number of modules in LOO-CV; GO:BP, GO:MF, GO:CC represent the GO biological process, GO molecular function, GO cellular component respectively, while Groups represents the domain groups annotated with each module, Terms represent the unique number of GO term; and Referenced represents GO terms previously reported in literature, #U Sum, Unique sum.