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Table 3 Top 50 genes with respect to M bw

From: Graph-theoretical comparison of normal and tumor networks in identifying BRCA genes

  Id Gene W bw N T M G S 1 G S 2 Top neighbors in MWIS
1 Q15796 SMAD2 0.896534 64 31 0 Yes Yes  
2 Q14164 IKBKE 0.646178 1 16 0 No No  
3 P54274 TERF1 0.638236 59 55 0 No No 1, 20, 34
4 P68400 CSNK2A1 0.626417 85 91 0 No No  
5 P04637 TP53 0.60796 98 97 17 Yes Yes 1, 4, 7, 8, 34, 42, 44
6 Q99750 MDFI 0.60268 60 36 0 No No  
7 P04183 TK1 0.578819 10 92 0 No No  
8 Q96SB4 SRPK1 0.457947 0 36 0 No No  
9 Q13526 PIN1 0.438312 68 77 0 No No 4, 6, 46
10 P46108 CRK 0.297179 96 70 0 No No 21, 25, 35
11 P62993 GRB2 0.284621 97 98 0 No No 2, 46
12 Q99558 MAP3K14 0.283214 45 17 0 No No  
13 Q9Y6K9 IKBKG 0.271303 4 10 0 No No 12, 19
14 Q13387 MAPK8IP2 0.269689 1 60 0 No No  
15 Q13233 MAP3K1 0.255928 68 63 4 No Yes  
16 Q09472 EP300 0.250913 94 89 0 Yes Yes 1, 34, 35
17 P21246 PTN 0.248842 53 2 0 No No  
18 P20333 TNFRSF1B 0.234258 71 31 0 No No  
19 Q99759 MAP3K3 0.233384 19 4 0 No No  
20 O60341 KDM1A 0.229576 79 93 0 No No  
21 Q92569 PIK3R3 0.225153 29 76 0 No No  
22 Q15714 TSC22D1 0.22131 99 76 0 No No 17, 42
23 Q92624 APPBP2 0.217109 41 38 0 No No 2
24 Q15047 SETDB1 0.212244 81 95 0 No No 7, 20
25 P30480 HLA-B 0.20772 99 99 0 No No  
26 P25791 LMO2 0.197168 38 2 0 No Yes  
27 P25786 PSMA1 0.194226 4 36 0 No No 2, 25, 40
28 P08238 HSP90AB1 0.187144 99 99 0 No No 2, 4, 8, 12, 15, 19, 34, 42, 49
29 P14921 ETS1 0.184287 82 42 0 No No  
30 P12757 SKIL 0.177551 32 73 1 No No 1
31 P03372 ESR1 0.175797 4 36 0 Yes Yes 15
32 Q16539 MAPK14 0.173795 60 33 0 No No 8
33 P63104 YWHAZ 0.172695 99 99 0 No No 7, 19, 42
34 P22736 NR4A1 0.170823 84 44 0 No No  
35 O15162 PLSCR1 0.169279 90 76 0 No No  
36 P12931 SRC 0.169016 4 28 0 No Yes 4, 21
37 P04626 ERBB2 0.164884 88 98 1 No Yes 8, 14, 21
38 P40337 VHL 0.158704 99 99 0 No Yes 6
39 Q96EB6 SIRT1 0.153643 94 68 1 Yes No 4
40 P40692 MLH1 0.147726 1 20 0 No Yes  
41 Q9Y4K3 TRAF6 0.145986 2 2 0 No No 12, 19
42 P04792 HSPB1 0.14386 99 99 0 No No  
43 Q5UIP0 RIF1 0.139848 26 20 1 No No 7, 42
44 Q96PM5 RCHY1 0.136242 42 22 1 No No  
45 Q92754 TFAP2C 0.135754 86 98 1 No No  
46 Q9Y478 PRKAB1 0.134543 98 96 0 No No  
47 O14920 IKBKB 0.132882 62 53 0 No Yes 12, 15, 19, 45
48 P21980 TGM2 0.132793 60 81 0 No No 1
49 Q9Y572 RIPK3 0.13256 92 75 0 No No  
50 P42858 HTT 0.131761 4 10 0 No No 21
  1. The first column provides the Uniprot id of the gene, the second column provides the gene name. The third column provides the weight of each gene based on M bw . The fourth and the fifth columns provide the number of instances each gene is expressed in the normal and tumor samples respectively. The sixth column provides the number of mutations of a gene observed throughout all the tumor samples in the dataset. The seventh column indicates whether the gene is listed in the breast cancer pathway of the first golden standard, the NCBI BioSystems, whereas the eight columnd indicates whether it is listed in the second golden standard, the COSMIC database. The last column provides the set of PPI network neighbors of the corresponding gene from the top 50 list that are also in MWIS