Table 2 Overlap analysis of Track-HD and Leiden cohorts shows that a significant excess of pathways are associated with HD (p < 0.05) in both datasets.

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

Reference dataset

Comparison dataset

Direction of dysregulation in HD

Number of pathways significant in both datasets (p value)

Generic pathways

HD brain modules

Control brain modules

Leiden

Track-HD

Nondirectional

69 (4.6E-02)

—

—

Downregulated

130 (<1.0E-03)

4 (1.1E-01)

24 (<1.0E-03)

Upregulated

219 (<1.0E-03)

9 (<1.0E-03)

23 (<1.0E-03)

Track-HD

Leiden

Nondirectional

69 (1.4E-01)

—

—

Downregulated

130 (1.7E-02)

4 (3.5E-02)

24 (<1.0E-03)

Upregulated

217 (<1.0E-03)

10 (<1.0E-03)

21 (<1.0E-03)

  1. Significance of overlap is greatest when directionality is taken into account. There is an excess of significantly enriched pathways and modules in the reference dataset conditional on the pathway being enriched (p < 0.05) in the comparison dataset. The generic pathways gene set is collated from publicly-available databases including GO and KEGG. HD brain modules are derived from Neueder and Bates30. Control brain modules are from the Braineac32 and Gibbs, et al.33 expression datasets.
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