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Table 5 Representative enriched GO categories and pathways in mRNA association modules

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

index drivers/regulators N 1 function p-value
44 ZIC1,MITF seg 18 CNV (+) 118 melanosome 1.300 × 10-7
45 TBP,MYB,HDAC2 seg 31 CNV (+) 77 RNA polymerase II regulation 1.35 × 10-5
45 TBP,MYB,HDAC2 seg 31 CNV (+) 77 condensed chromosome 7.928 × 10-5
46 SREBF2,EP300 seg 84 CNV (+) 49 cholesterol biosynthesis 3.781 × 10-4
47 E2F3,NFYA,SRF seg 30 CNV (+) 31 ceramide signaling pathway 4.302 × 10-5
47 E2F3,NFYA,SRF seg 30 CNV (+) 31 NFKB signaling pathway 8.632 × 10-4
48 TCF7L2 seg 42 CNV (+) 30 multi-drug resistance factors 5.884 × 10-5
48 TCF7L2 seg 42 CNV (+) 30 positive regulation of epithelial cell proliferation 1.096 × 10-4
49 NR2C1,NFYB seg 49 CNV (+) 22 mRNA translation 2.314 × 10-4
54 UBP1 seg 16 CNV (+) 18 RNA Pol II phosphorylation 4.429 × 10-4
56 APEX1 seg 57 (+) 16 cleavage of growing transcript 7.872 × 10-4
57 RPA2,EIF2C1 seg 16 CNV (+) 15 mRNA splicing 1.945 × 10-6
57 RPA2,EIF2C1 seg 16 CNV (+) 15 mRNA Pol II transcription initiation 7.260 × 10-4
59 RICS seg 51 CNV (+) 14 regulation of apoptosis 1.397 × 10-4
62 APC mutation (+) 136 liver development 4.932 × 10-4
66 TP53 mutation (-) 35 caspase activation 1.101 × 10-3
66 TP53 mutation (-) 35 P53 signaling pathway 4.138 × 10-4
68 TP53 mutation (+) 33 cell cycle 9.787 × 10-4
69 CDKN2A mutation (+) 32 cell motility 8.510 × 10-4
70 KRAS mutation (+) 25 DNA replication 2.689 × 10-3
71 PTEN mutation (+) 20 JNK cascade 2.904 × 10-4
75 PTEN mutation (-) 13 positive regulation of I-κB kinase/NF-κB cascade 1.745 × 10-3
79 CCND1,PPARG methylation (-) 13 negative regulation of cell proliferation 6.074 × 10-3
81 mir group 1 (-) 121 transport vesicle 3.297 × 10-4
82 mir group 2 (-) 121 translation 3.694 × 10-4
83 TF group 1 (+) 338 integrin signaling pathway 4.664 × 10-8
83 TF group 1 (+) 338 TGFβ signaling pathway 9.555 × 10-4
84 TF group 2 (+) 338 T cell differentiation 1.128 × 10-4
  1. Index: module index. N1: number of passengers in the module. Function: enriched GO category or pathway. p-value: hyper-geometric p-value for enrichment. 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,RBMS. TF group 2 consists of ERG,ELK4,NFATC1,POU5F1,ZNF350.