Table 3.
WGCNA Co-expression module characteristics.
| Modulea | #genes | Module eigengene significantb | DEG enrichmentc | Cell type enrichmentd | Top genese | Lore QTLf | DEGg |
|---|---|---|---|---|---|---|---|
| black | 165 | Region (2.13E-05) | Matk | ||||
| Kcnh3 | |||||||
| Psd | |||||||
| Tmem191c | |||||||
| Ppp2r2c | |||||||
|
| |||||||
| yellow | 299 | Strain (4.12E-04) | ST (2.60E-04) WB (5.26E-07) |
Ptprn | Lore1 | ||
| Eif3k | |||||||
| Glt25d1 | |||||||
| Tnip1 | |||||||
| Tpd52 | |||||||
|
| |||||||
| brown | 1082 | Region (1.11E-03) | Oligodendrocyte (2.31E-07) | Rps6ka4 | |||
| Gsn | |||||||
| Rbx1 | |||||||
| Ephb1 | |||||||
| Icam5 | |||||||
|
| |||||||
| cyan | 76 | ST (3.66E-04) | Robo3 | ST | |||
| Kalrn | |||||||
| Kcns1 | Lore2b | ST | |||||
| Cacnb3 | |||||||
| Sytl2 | |||||||
|
| |||||||
| greenyellow | 171 | Strain (6.63E-06) Region (2.37E-04) |
ST (9.10E-04) | 6030458C11Rik | ST | ||
| Selplg | ST, WB | ||||||
| 4933439F18Rik | ST | ||||||
| 4632428N05Rik | |||||||
| Gm10116 | |||||||
|
| |||||||
| magenta | 87 | Strain (2.26E-07) | ST (2.60E-04) WB (1.45E-10) |
Gm10516 | ST, WB | ||
| Folh1 | WB | ||||||
| Prss50 | WB | ||||||
| Rnasel | ST, WB | ||||||
| 4930452B06Rik | |||||||
|
| |||||||
| grey60 | 36 | Strain (1.39E-04) | 2610002J02Rik | ||||
| Polr1b | Lore2a | ||||||
| Lama2 | |||||||
| Chi3l1 | |||||||
| Adi1 | |||||||
|
| |||||||
| darkred | 24 | WB (4.23E-02) | Rnd2 | Lore4 | |||
| Uchl1 | |||||||
| Add1 | |||||||
| Ncan | |||||||
| Tstd2 | |||||||
|
| |||||||
| green | 123 | Strain (1.78E-07) | ST (1.48E-04) WB (7.10E-06) |
Tmem181a | |||
| A530054K11Rik | ST, WB | ||||||
| Copb1 | ST | ||||||
| Tmem181b-ps | ST | ||||||
| Trmt6 | Lore2a | ||||||
|
| |||||||
| blue | 3211 | Strain (2.20E-03) Region (2.01E-06) |
ST (2.51E-02) | Rasgrp1 | |||
| Ppp1r9a | |||||||
| Pde7b | ST | ||||||
| Nexn | LoreChr3 | ST | |||||
| Rgs4 | ST | ||||||
|
| |||||||
| turquoise | 8288 | Region (1.63E-06) | Neuron (5.45E-04) Astrocyte (2.07E-02) |
Gm672 | |||
| Kndc1 | ST | ||||||
| Pcdh1 | |||||||
| Plxna1 | ST | ||||||
| Slc20a2 | |||||||
a
Gene co-expression module produced by WGCNA. Modules not significant for eigengene difference, DEG or cell-type enrichment are not shown.
b
Results of Analysis of Variance of the first principle component, or module eigengene, of expression values for each module. Each module eigengene was tested across strain and region.
c
Module over-representation of DEGs from either ST or WB.
d
Module over-representation of genes expressed at least 3-fold higher in specific cell types, neurons, astrocytes, or oligodendrocytes (Cahoy et al, 2008).
e
The top five most interconnected genes in each module.
f
Lore QTL region containing corresponding top gene.
g
Region of differential expression of corresponding top gene.