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Table 4 Summary of co-citations in mRNA and microRNA association modules

From: Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines

mRNA modules     
index drivers/regulators N 1 N 2 N 3
44 ZIC1,MITF seg 18 CNV (+) 118 14 6
45 TBP,MYB,HDAC2 seg 31 CNV (+) 77 28 20
46 SREBF2,EP300 seg 84 CNV (+) 49 3 2
47 E2F3,NFYA,SRF seg 30 CNV (+) 31 5 4
48 TCF7L2 seg 42 CNV (+) 30 1 3
54 UBP1 seg 16 CNV (+) 18 1 0
62 APC mutation (+) 136 17 10
63 APC mutation (-) 56 3 6
65 CDNK2A mutation (-) 43 3 6
66 TP53 mutation (-) 35 11 3
67 BRAF mutation (-) 34 3 3
68 TP53 mutation (+) 33 4 6
69 CDKN2A mutation (+) 32 6 3
71 PTEN mutation (+) 20 1 2
72 KRAS mutation (-) 16 1 1
73 BRAF mutation (+) 16 3 1
75 PTEN mutation (-) 13 2 4
76 PAX8 methylation (-) 67 1 4
77 BCR methylation (-) 58 5 10
79 CCND1,PPARG methylation (-) 13 4 7
80 COL5A1 methylation (-) 10 1 1
83 TF group 1 (+) 338 236 48
microRNA modules     
index drivers/regulators N1 N2 N3
4 ZIC1,MITF seg 18 CNV (-) 19 3 5
5 DNMT1 seg 15 CNV (+) 15 1 2
6 SRF seg 30 CNV (+) 13 1 1
7 MAP2K4 seg 66 CNV (-) 13 2 2
10 TP53 mutation (+) 17 3 3
12 APC mutation (+) 10 1 1
14 BCR methylation (-) 12 1 4
15 SMAD3,BDNF (+) 28 8 10
20 HIF1A (+) 14 1 2
  1. Index: module index. N1: number of passengers in the module. N2: number of co-cited driver/regulator-passenger pairs in the module. N3: max number of co-cited driver/regulator-passengers over 10 random modules of the same size. TF group 1 consists of SMAD3,FOXD1,PLAU,BDNF,FOSL2,FOSL1,RBMS. TF group 2 consists of ERG,ELK4,NFATC1,POU5F1,ZNF350.
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BMC Systems Biology

ISSN: 1752-0509

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