Table 4 The 10 most significantly up and downregulated WGCNA brain expression modules in HD versus control blood.

From: Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease

Direction of dysregulation in HD

Brain expression gene set

Module

Brain region

Annotation

Number of genes

p (Combined)

p (Track-HD)

p (Leiden)

Upregulated

HD

111

FC BA9

Immune response

514

7.8E-12

1.3E-04

7.5E-05

HD

69 (FC4pos1)

FC BA4

Inflammatory response

712

3.8E-08

3.1E-05

1.3E-03

Control (Braineac)

712

TCTX

Inflammatory response

213

1.4E-07

3.4E-05

8.1E-04

HD

48 (CNpos2)*

CN

Lipid metabolism/regulation of transcription

1785

2.0E-07

3.9E-03

6.3E-03

Control (Braineac)

110

FCTX

Inflammatory response

173

8.9E-07

1.0E-03

2.5E-03

Control (Braineac)

909

White Matter

Activation of immune response

265

2.1E-06

1.2E-03

2.5E-02

Control (Braineac)

610

Substantia Nigra

Inflammatory response

178

1.2E-05

8.6E-04

5.6E-04

Control (Braineac)

811

Thalamus

Inflammatory response

142

1.6E-05

3.9E-03

2.9E-03

Control (Gibbs)

56

Pons

Lipoprotein/ immune response /GTPase regulator activity

207

2.0E-05

2.4E-04

4.2E-02

Control (Braineac)

911

White Matter

Inflammatory response

159

3.0E-05

8.4E-04

1.4E-02

Downregulated

Control (Gibbs)

22

CB

Pro-rich region

831

1.8E-08

2.5E-03

2.1E-02

Control (Gibbs)

28

FC

Intra-cellular transport/mitochondrion

3178

2.1E-08

6.3E-04

7.7E-05

Control (Braineac)

304

Medulla

mRNA metabolic process

1811

2.9E-08

5.0E-15

4.0E-02

HD

66 (CNneg1)*

CN

Synapse/ion channels

2645

2.7E-07

1.5E-04

2.1E-02

Control (Braineac)

804

Thalamus

Regulation of cell morphogenesis

857

1.3E-06

4.0E-02

4.1E-04

Control (Braineac)

522

Putamen

Regulation of RNA splicing

64

4.4E-06

6.3E-03

2.7E-04

Control (Gibbs)

74

Pons

Transcription/acetylation/protein transport

1183

9.2E-06

3.9E-08

7.4E-04

Control (Braineac)

702

TCTX

Antigen processing: ubiquitination and proteasome degradation

4602

3.9E-04

1.2E-03

2.5E-02

Control (Gibbs)

48

FC

Transcription corepressor/cell morphogenesis

648

4.7E-04

7.8E-03

2.1E-02

Control (Braineac)

202

Hippocampus

Mitochondrial membrane

2737

4.8E-04

1.2E-07

1.5E-02

  1. All modules in this table are significantly dysregulated after correction for multiple testing (q < 0.05) in the combined blood sample. HD brain modules were defined by Neueder and Bates30, and Control brain modules were generated from Braineac32 and Gibbs, et al.33. Neueder and Bates30 module identifiers are given in brackets where available. *Denotes the caudate modules that were highly positively and negatively Neueder and Bates30. CN – caudate nucleus; FC – frontal cortex; FC BA4 – BA4 region of the frontal cortex; FC BA9 – BA9 region of the frontal cortex; CB – cerebellum; TCTX – temporal cortex.
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