Table 1.
| Main Effect (p-value)a | Module | genes | Cell Type Enrichment (p-value)b | QTL Enrichment (p-value)c | Functional Enrichmentd | Notable Genese |
|---|---|---|---|---|---|---|
| Ethanol (0.019) | coral2 | 77 | Neuron (0.046) | Lore5 (0.022) Aaq1 (0.0081) |
ribosome, acetylation | Pmm1, Rangap1 |
| Ethanol (0.02) | red | 629 | acetylation, phosphoprotein, nucleotide binding | Kirrel | ||
| Interaction (0.000037)* | darkseagreen4 | 498 | Lore4 (0.045) Lore1 (0.0083)* |
alternative splicing, metal ion binding | Jph4, Ptprn, Acr | |
| Interaction (0.012) | firebrick4 | 61 | Neuron (6.6x10-12)* | Lore5 (0.012) Aaq1 (0.0042)* |
ion channel activity | Baiap3, Wdr6, Gdap1l1, Adcy8, Oxtr, Crh, Stx12, Chgb, Trhr, Oprm1 |
| Interaction (0.013) | darkred | 181 | Astrocyte (0.0055) Oligodendrocyte (0.035) |
Ap1q (0.0033)* | extracellular matrix, secreted protein | Slc2a12, Gpx8, Stk38l |
| Interaction (0.014) | darkviolet | 56 | apoptosis | Snx5, Nkap, Negr1 | ||
| Interaction (0.016) | skyblue | 160 | Ap1q (0.039) | nucleus, RNA processing | Plxnb2, Luzp1 | |
| Interaction (0.017) | darkolivegreen4 | 59 | Neuron (0.00065)* Astrocyte (0.0076) |
ribonucleotide binding | Sag, Acvr2a, Stx7 | |
| Interaction (0.019) | steelblue | 154 | Oligodendrocyte (p<1x10-13)* Astrocyte (0.017) |
Etact1 (0.016) | amino acid transport/metabolism, myelin sheath | Mdk, Nkain1, Ppap2c, Rassf2, Hapln2, Trf, Carhsp1 |
| Interaction (0.032) | brown | 1191 | Ap3q (0.023) Etact2 (0.015) |
transcriptional regulation, signaling (neurotrophin, Wnt, MAPK, ErbB, Notch), ion channels | Nedd4l, Polr2a | |
| Running (0.00002)* | blue2 | 57 | Oligodendrocyte (0.000036)* | Ap3q (0.0035)* | ion transport, metabolic processes | Mal |
| Running (0.00015)* Ethanol (0.05) |
darkolivegreen | 149 | metal ion binding, alternative splicing | Chrna7, Cacna1e, Siae | ||
| Running (0.0003)* Interaction (0.023) |
magenta | 450 | ribosome, translation, neurodegenerative diseases | Hyal2, Aurkaip1, Ncaph2, Ssb | ||
| Running (0.00033)* Interaction (0.0093) |
darkturquoise | 408 | Etact2 (0.035) | transcriptional regulation | Nln, Ramp3, Fcgrt | |
| Running (0.00073)* Interaction (0.014) |
mediumorchid | 75 | acetylation, nuclear lumen | Uchl1, Myl12a, Lamb2 | ||
| Running (0.00074)* | darkmagenta | 149 | Astrocyte (0.0059) | Ap3q (0.046) | phosphoprotein, acetylation | Aldh3b1, Syt1 |
| Running (0.0016) | black | 803 | Astrocyte (0.0024) | Etact1 (0.019) Lore1 (0.03) |
nucleus, ribonucleotide binding | Ogfr, Ramp1 |
| Running (0.0028) | lavenderblush2 | 261 | Neuron (0.00055)* | Lore4 (0.0053)* | phosphoprotein, plexin, synaptosome | Nav1, Syn1, Camta2, Bsn, Vamp2, Kcnj10, Rab6b, Cabin1, St8sia1, Prrg3, Crhr1, Prkcg |
| Running (0.0031) | antiquewhite4 | 359 | protein transport, mitochondria | Eif3e, Cdkn2c | ||
| Running (0.011) | cyan | 605 | mitochondrial processes, neurodegenerative disease | Fbln2, Tmem159 | ||
| Running (0.013) | lightyellow | 555 | metal ion binding, alternative splicing, cell junction | Lonrf2, Nyap2, Thrb, Mdm4, Kcnq3, Myo9a | ||
| Running (0.015) Ethanol (0.019) |
purple | 316 | RNA processing, transcriptional regulation | Crabp1. Ssrp1, S1pr5, Dnm2, Ntng1, Hdac8 | ||
| Running (0.026) | mediumpurple2 | 117 | Neuron (0.0015)* | Ap1q (0.014) Aaq1 (0.025) |
membrane, vesicle, synapse | Itga4, Dcx, Lrfn5, Rasgrp1, Dzank1, Cadm2, Sorbs2, Slc19a2 |
| Running (0.027) Ethanol (0.0046) |
green | 539 | Lore4 (0.00053)* | membrane, transport, transmembrane region | Stx16, Kcnh4, Nrros, Nrsn2, Stx3, Slc25a11, Ntrk3, Slc6a8 | |
| Running (0.04) | sienna3 | 246 | Neuron (8.4x10-13)* | Ap5q (0.0068) | synapse, cell junction, axon guidance, potassium ion transport, ion channel activity | Etl4, Sncb, Stxbp1, Rassf5, Slc4a8, Mast1, Kcnc1 |
| Running (0.04) | skyblue2 | 74 | Oligodendrocyte (0.038) | ubiquitination | Pla2g4a, Drd1, Hes5 |
a
Module eigengene significance for main effects and/or interaction, determined by ANOVA of log2 normalize module eigengene.
b
Over-represented cell-types, using data from Cahoy et al (2008). P-values bases on one tail hypergeometric test.
c
Over-represented ethanol related quantitative trait loci. P-values bases on one tail hypergeometric test.
d
Over-represented functional groups. Assessed using DAVID.
e
Notable genes were determined by high module membership, gene-trait significance, brain expression, or ethanol QTL.
*
p-values significant when corrected for number of tests.