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Table 1 Summary information of association modules for mRNA expressions

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

index driver type drivers reg sign N index driver type drivers reg sign N
1 intra CNV seg 30 (chr 6p) NA + 84 44 inter CNV seg 18 (chr 3p) ZIC1,MITF + 118
2 intra CNV seg 54 (chr 12q) NA + 77 45 inter CNV seg 31 (chr 6q) TBP,MYB,HDAC2 + 77
3 intra CNV seg 1 (chr 1p) NA + 74 46 inter CNV seg 84 (chr 22q) SREBF2,EP300 + 49
4 intra CNV seg 57 (chr 14q) NA + 62 47 inter CNV seg 30 (chr 6p) E2F3,NFYA,SRF + 31
5 intra CNV seg 69 (chr 17q) NA + 62 48 inter CNV seg 42 (chr 10q) TCF7L2 + 30
6 intra CNV seg 11 (chr 2p) NA + 58 49 inter CNV seg 55 (chr 12q) NR2C1,NFYB + 22
7 intra CNV seg 42 (chr 10q) NA + 55 50 inter CNV seg 19 (chr 3q) ZNF148 + 22
8 intra CNV seg 3 (chr 1p) NA + 53 51 inter CNV seg 63 (chr 16pq) NFATC3,RBL2 + 21
9 intra CNV seg 37 (chr 8q) NA + 53 52 inter CNV seg 69 (chr 17q) SPOP,NME2,POLG2 + 20
10 intra CNV seg 59 (chr 14q) NA + 53 53 inter CNV seg 42 (chr 10q) NFKB2 + 19
11 intra CNV seg 16 (chr 3p) NA + 49 54 inter CNV seg 16 (chr 3p) UBP1 + 18
12 intra CNV seg 63 (chr 16pq) NA + 49 55 inter CNV seg 83 (chr 22q) EWSR1 + 17
13 intra CNV seg 33 (chr 7q) NA + 47 56 inter CNV seg 57 (chr 14q) APEX1 + 16
14 intra CNV seg 84 (chr 22q) NA + 47 57 inter CNV seg 16 (chr 3p) RPA2,EIF2C1 + 15
15 intra CNV seg 55 (chr 12q) NA + 44 58 inter CNV seg 19 (chr 3q) CNBP + 15
16 intra CNV seg 51 (chr 11q) NA + 43 59 inter CNV seg 51 (chr 11q) RICS + 14
17 intra CNV seg 2 (chr 1p) NA + 42 60 inter CNV seg 56 (chr 13q) GTF3A + 13
18 intra CNV seg 73 (chr 19p) NA + 42 61 inter CNV seg 4 (chr 1q) RUNX3 + 10
19 intra CNV seg 50 (chr 11q) NA + 40 62 mutation APC NA + 136
20 intra CNV seg 68 (chr 17q) NA + 39 63 mutation APC NA - 56
21 intra CNV seg 65 (chr 17p) NA + 37 64 mutation PIK3CA NA + 50
22 intra CNV seg 32 (chr 7p) NA + 36 65 mutation CDKN2A NA - 43
23 intra CNV seg 35 (chr 7q) NA + 35 66 mutation TP53 NA - 35
24 intra CNV seg 31 (chr 6q) NA + 33 67 mutation BRAF NA - 34
25 intra CNV seg 19 (chr 3q) NA + 32 68 mutation TP53 NA + 33
26 intra CNV seg 18 (chr 3p) NA + 30 69 mutation CDKN2A NA + 32
27 intra CNV seg 9 (chr 1q) NA + 29 70 mutation KRAS NA + 25
28 intra CNV seg 22 (chr 4p) NA + 29 71 mutation PTEN NA + 20
29 intra CNV seg 62 (chr 15q) NA + 29 72 mutation KRAS NA - 16
30 intra CNV seg 41 (chr 9q) NA + 28 73 mutation BRAF NA + 16
31 intra CNV seg 49 (chr 11q) NA + 28 74 mutation PIK3CA NA - 13
32 intra CNV seg 56 (chr 13q) NA + 28 75 mutation PTEN NA - 13
33 intra CNV seg 60 (chr 15q) NA + 28 76 methylation PAX8 NA - 61
34 intra CNV seg 44 (chr 11p) NA + 27 77 methylation BCR NA - 58
35 intra CNV seg 61 (chr 15q) NA + 26 78 methylation HOXC13 NA - 19
36 intra CNV seg 80 (chr 21q) NA + 24 79 methylation CCND1,PPARG NA - 13
37 intra CNV seg 36 (chr 8p) NA + 23 80 methylation COL5A1 NA - 10
38 intra CNV seg 27 (chr 5q) NA + 22 81 microRNA mir group 1 NA - 121
39 intra CNV seg 39 (chr 9p) NA + 22 82 microRNA mir group 2 NA - 120
40 intra CNV seg 12 (chr 2q) NA + 20 83 TF TF group 1 NA + 338
41 intra CNV seg 74 (chr 19q) NA + 20 84 TF TF group 2 NA + 338
42 intra CNV seg 83 (chr 22q) NA + 20       
43 intra CNV seg 85 (chr 23pq) NA + 20       
  1. Index: module index. Reg: intermediate regulators. Sign: the functional direction (activation or repression) from drivers to passengers. N: number of passenger genes. Intra CNV: intra-segment CNV. Inter CNV: inter-segment CNV. TF: transcription factor expressions. The locations of segments are reported in Supplementary Table S5. Mir group 1 consists of mir-92,mir-96,mir-106a,mir 20b,mir-17,mir-19b,mir-32,mir-135,mir-25,mir-106b,mir-93,mir-106,mir-18,mir-20. Mir group 2 consists of mir-24,mir-99b,mir-27b,mir-21,mir-125a,mir-23b,mir-27a,mir-23a. TF group 1 consists of SMAD3,FOXD1,PLAU,BDNF,FOSL2,FOSL1,RBMS1. TF group 2 consists of ERG,ELK4,NFATC1,RFX3,POU5F1,ZNF350.
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BMC Systems Biology

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