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. 2014 Jun 28;20(24):7894–7913. doi: 10.3748/wjg.v20.i24.7894

Table 3.

Pathways and molecular functions regulated by methylation-silenced microRNA gene targets

No. Panther Genes Gene Contrib
GO molecular function1
1 Binding (GO:0005488) 2799 40.60% 33.80%
2 Catalytic activity (GO:0003824) 2126 30.80% 25.70%
3 Transcription regulator activity (GO:0030528) 920 13.30% 11.10%
4 Receptor activity (GO:0004872) 696 10.10% 8.40%
5 Structural molecule activity (GO:0005198) 558 8.10% 6.70%
6 Enzyme regulator activity (GO:0030234) 494 7.20% 6.00%
7 Transporter activity (GO:0005215) 418 6.10% 5.00%
8 Ion channel activity (GO:0005216) 152 2.20% 1.80%
9 Translation regulator activity (GO:0045182) 57 0.80% 0.70%
10 Motor activity (GO:0003774) 53 0.80% 0.60%
GO Biological process2
1 Metabolic process (GO:0008152) 3277 47.50% 20.80%
2 Cellular process (GO:0009987) 2564 37.20% 16.30%
3 Cell communication (GO:0007154) 1793 26.00% 11.40%
4 Developmental process (GO:0032502) 1315 19.10% 8.40%
5 Transport (GO:0006810) 1190 17.30% 7.60%
6 Immune system process (GO:0002376) 956 13.90% 6.10%
7 System process (GO:0003008) 927 13.40% 5.90%
8 Cell cycle (GO:0007049) 797 11.60% 5.10%
9 Cellular component organization (GO:0016043) 630 9.10% 4.00%
10 Response to stimulus (GO:0050896) 613 8.90% 3.90%
GO cellular component3
1 Intracellular (GO:0005622) 486 7.10% 50.40%
2 Extracellular region (GO:0005576) 233 3.40% 24.10%
3 Plasma membrane (GO:0005886) 86 1.20% 8.90%
4 Ribonucleoprotein complex (GO:0030529) 84 1.20% 8.70%
5 Protein complex (GO:0043234) 76 1.10% 7.90%
GO protein class4
1 Nucleic acid binding (PC00171) 1144 16.60% 12.60%
2 Transcription factor (PC00218) 920 13.30% 10.20%
3 Hydrolase (PC00121) 691 10.00% 7.60%
4 Receptor (PC00197) 690 10.00% 7.60%
5 Transferase (PC00220) 662 9.60% 7.30%
6 Enzyme modulator (PC00095) 634 9.20% 7.00%
7 Signaling molecule (PC00207) 481 7.00% 5.30%
8 Transporter (PC00227) 457 6.60% 5.00%
9 Cytoskeletal protein (PC00085) 402 5.80% 4.40%
10 Kinase (PC00137) 316 4.60% 3.50%
Pathway5
1 Gonadotropin releasing hormone receptor pathway (P06664) 159 2.30% 4.80%
2 Wnt signaling pathway (P00057) 156 2.30% 4.70%
3 Inflammation mediated by chemokine and cytokine signaling pathway (P00031) 134 1.90% 4.00%
4 Integrin signalling pathway (P00034) 116 1.70% 3.50%
5 Angiogenesis (P00005) 98 1.40% 3.00%
6 EGF receptor signaling pathway (P00018) 84 1.20% 2.50%
7 Cadherin signaling pathway (P00012) 80 1.20% 2.40%
8 Huntington disease (P00029) 77 1.10% 2.30%
9 TGF-beta signaling pathway (P00052) 73 1.10% 2.20%
10 PDGF signaling pathway (P00047) 74 1.10% 2.20%
KEGG
hsa01100 metabolic pathways (434)
hsa05200 pathways in cancer (189)
hsa04151 PI3K-Akt signaling pathway (162)
hsa04010 MAPK signaling pathway (137)
hsa05205 proteoglycans in cancer (134)
hsa05166 HTLV-I infection (123)
hsa04510 Focal adhesion (116)
hsa04810 regulation of actin cytoskeleton (115)
hsa05202 transcriptional misregulation in cancer (100)
hsa04144 endocytosis (100)
1

Total genes n = 6893, total function hits n = 8282;

2

Total genes n = 6893, total process hits n = 15740;

3

Total genes n = 6893, total component hits n = 965;

4

Total genes n = 6893, total protein classess n = 9050;

5

Total genes n = 6893, total pathway hits n = 3313. Contrib: Contribution; PI3K: Phosphatidylinositol-3-kinase; MAPK: Mitogen-activated protein kinase; HTLV: Human T-lymphotropic virus 1; EGF: Epidermal growth factor; PDGF: Platelet-derived growth factor; TGF-β: Transforming growth factor beta.