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Table 3 The highest G-score networks and corresponding processes identified using MetaCore [50]

From: Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)

Networks GO Processes‡ Significantly changed genes involved p-value G-score
Ephrin-B receptors,
Ephrin-A receptors,
Connexin 32,
Twinfilin,
FXR1/2
cell projection organization and biogenesis (43.8%; 1.652e-19)
cell projection morphogenesis (43.8%; 1.723e-19)
cell part morphogenesis (43.8%; 1.723e-19)
cell morphogenesis (45.8%; 1.974e-18)
cellular structure morphogenesis (45.8%; 1.974e-18)
Receptors: Ephrin-B receptors ↑; Ephrin-B receptor 4 ↑; Ephrin-A receptors ↑
Regulators: Vav2 ↑
Binding Protein: Twinfillin ↓; Alpha Actin ↑
Channels: Connexin 32↑
Protein: FXR1/2 ↑; VAMP4 ↑
GTPase: CDC42 ↑
7.00e-11 91.44
FXR,
FXR/RXR-α,
GIPC,
SOX3,
Pitpnm (NIR2)
V(D)J recombination (6.8%; 5.712e-06)
response to stimulus (56.8%; 1.109e-05)
B cell homeostatic proliferation (4.5%; 2.286e-05)
organ morphogenesis (25.0%; 2.353e-05)
bile acid metabolic process (6.8%; 4.487e-05)
Transcription Factor: SOX3 ↑; TITF1 ↑↓; FXR ↑
Receptors: Syndecan-1 ↓
Binding Protein: Fetulin-A ↑; Pitpnm (NIR2) ↑↓; GIPC ↑; SYNE2 ↑; Actin ↑; RAD23A ↑↓
Channels: Kir3.3 ↑
Transporter: SLC6A6 ↑↓; Glut1 ↓
Protein: COQ4 ↑
Lipid Kinase: P3C2B ↑; PI3K class II ↑
3.08e-23 36.22
SET1A,
Autophagin-1,
ASNS,
ETV6(TEL1),
POP1 (RNase P/MRP subunit)
tRNA catabolic process (7.7%; 2.622e-06)
tRNA 5'-leader removal (7.7%; 7.859e-06)
ncRNA catabolic process (7.7%; 1.570e-05)
autophagy (11.5%; 2.111e-05)
intracellular transport (30.8%; 1.049e-04)
Transcription Factor: ETV6 (Tel1) ↑
Binding Protein: PEX3 ↑;FXR 2↑; Histone H2A ↑
Protease: Autophagin-1↑
Enzyme: GSHB ↑; ASNS ↑; Set1A ↑; POP1 (RNaseP/MRP subunit) ↑
Protein: ES1 ↑
1.66e-20 35.43
NF-kB,
Large 39 S subunit,
MRPL16,
2'-5'-oligoadenylate synthetase,
TIEG
response to UV (27.3%; 3.661e-10)
nucleotide-excision repair, DNA damage removal (18.2%; 3.547e-08)
nucleotide-excision repair, DNA incision (13.6%; 1.320e-07)
DNA catabolic process, endonucleolytic (13.6%; 1.978e-07)
response to light stimulus (27.3%; 2.314e-07)
Transcription Factor: TIEG ↑
Binding Protein: Fetulin-A ↑; MRPL16 ↓; MRPL37 ↓ XPA ↑; P21 ↑
Enzyme: 2'-5' oligoadenylate synthetase ↑
SULT1A1 ↑
Kinase: PRKX ↑
1.45e-17 35.39
  1. ‡ (% refers to objects on network belonging to process; p-value showing statistical significance of the GO process on that network)