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Table 2 Gain of significance in enriched pathways

From: Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition

Up-regulated Down-regulated
Pathway Delta Pathway Delta
protein folding 5.77 DNA packaging complex 3.76
‘de novo’ protein folding 5.73 basement membrane 3.47
unfolded protein binding 5.54 positive regulation of epithelial cell proliferation 2.52
chaperone-mediated protein folding 5.32 negative regulation of gliogenesis 2.49
‘de novo’ posttranslational protein folding 4.68 fatty acid beta-oxidation 2.30
heat shock protein binding 4.34 nucleosome 2.18
response to unfolded protein 4.10 glomerulus development 2.16
response to topologically incorrect protein 3.53 aorta development 2.06
oxidoreductase activity, acting on paired… 2.74 endothelium development 1.95
Up-regulated Down-regulated
Pathway Delta Pathway Delta
positive regulation of cardiac muscle tissue dev… 1.99 tertiary granule 5.22
regulation of smooth muscle cell differentiation 1.98 ficolin-1-rich granule membrane 5.00
negative regulation of protein serine/threonine kin… 1.98 regulation of myeloid leukocyte mediated immunity 4.55
hormone-mediated signaling pathway 1.95 regulation of leukocyte degranulation 4.34
lung alveolus development 1.71 specific granule 4.22
positive regulation of striated muscle tissue dev… 1.69 ficolin-1-rich granule 4.15
positive regulation of muscle organ development 1.69 tertiary granule membrane 3.57
positive regulation of muscle tissue development 1.62 regulation of mast cell activation 3.52
negative regulation of MAP kinase activity 1.48 vacuolar lumen 3.05
regulation of cardiac muscle cell differentiation 1.48 regulation of mast cell degranulation 3.05
  1. Tables representing the top 10 pathways with the highest delta for up- and down-regulated pathways for both cohorts. The delta value represents the change in the enrichment –log10 (p-value) between the results with and without MGP adjustment (positive values imply an increase in p-value when accounting for cellularity). Complete results are provided in Additional file 6