Table 3 Pathways enriched with ethanol-responsive genes from four co-expression modules

From: EFhd2/Swiprosin-1 is a common genetic determinator for sensation-seeking/low anxiety and alcohol addiction

Pathway

N

FDR

Genes

Upregulated genes (yellow module)

 Lysine degradation

8

2.25E−07

Ehmt2, Setdb1, Plod1, Tmlhe, Whsc1l1, Gcdh, Ogdh, Plod2

 Chemokine signalling pathway

13

6.72E−07

Pik3r5, Arrb2, Prkcd, Mapk3, Stat5b, Gnb1, Arrb1, Vav2, Ptk2b, Ptk2, Akt1, Stat3, Stat1

 Natural killer-cell-mediated cytotoxicity

9

3.18E−05

Pik3r5, Mapk3, H2-D1, Itgb2, Lcp2, Fcer1g, Icam1, Vav2, Ptk2b

 PPAR signalling pathway

7

7.99E−05

Lpl, Rxra, Slc27a4, Acox1, Scd1, Slc27a1, Cpt1c

 Calcium signalling pathway

10

1.05E−04

Phkg1, Itpkb, Pde1b, Phka2, Mylk3, Grm1, Phkg2, Ptk2b, Camk2b, Adra1b

 Glycerophospholipid metabolism

6

6.39E−04

Chkb, Lpcat2, Agpat6, Pnpla6, Mboat7, Pla2g2d

 Inositol phosphate metabolism

5

8.91E−04

Inppl1, Inpp5a, Itpkb, Inpp5k, Isyna1

 Jak–STAT signalling pathway

8

9.49E−04

Osmr, Pik3r5, Il7, Stat5b, Akt1, Il10rb, Stat3, Stat1

 Long-term potentiation

5

1.73E−03

Mapk3, Rps6ka1, Grm1, Camk2b, Gria1

 Phosphatidylinositol signalling system

5

3.03E−03

Inppl1, Pik3r5, Inpp5a, Itpkb, Inpp5k

 mRNA surveillance pathway

5

5.18E−03

Upf3b, Casc3, Smg6, Acin1, Upf1

 Glutamatergic synapse

6

5.66E−03

Mapk3, Grm1, Gnb1, Pla2g2d, Dlg4, Gria1

Downregulated genes (tan, pink, and purple modules)

 MAPK signalling pathway

17

8.26E−07

Pdgfa, Fgf9, Map2k6, Gadd45b, Ptprr, Gadd45g, Nr4a1, Fgf5, Dusp1, Kras, Fos, Dusp5, Dusp6, Jun, Map3k14, Nras, Rras2

 Tight junction

10

3.97E−05

Gnai1, Myl9, Ctnna2, Ppp2r2d, Myh2, Pard6b, Kras, Cask, Nras, Rras2

 Osteoclast differentiation

9

7.97E−05

Nfkbia, Fosb, Map2k6, Fosl2, Junb, Fos, Jun, Map3k14, Socs3

 Regulation of actin cytoskeleton

11

4.80E−04

Pdgfa, Fgf9, Myl9, Itga1, Itgae, Fgf5, Kras, Pip5k1b, Arpc3, Nras, Rras2

 Cell cycle

8

6.51E−04

Gadd45b, Gadd45g, Ccne2, Cdkn2c, Cdk6, Ccnb2, Ccnh, Ccna1

 B-cell receptor signalling pathway

6

1.05E−03

Nfkbia, Kras, Fos, Cd72, Jun, Nras

 Axon guidance

7

4.06E−03

Efna2, Gnai1, Rnd1, Kras, Cxcl12, Met, Nras

  1. Abbreviations: ANOVA, analysis of variance; FDR, false discovery rate; GO, gene ontology; mRNA, messenger RNA.
  2. For each module, the table lists its size (number of genes), phenotypic association using the ANOVA model for the genotype, treatment and genotype × treatment interaction, GO term, number of genes from the module that are included in the listed GO term (N), and enrichment P-value. For each module, only the top term is listed.