Table S2.

KEGG pathways in which transcriptionally regulated genes are overrepresented in Alzheimer’s disease, clinical depression, or aging

KEGG pathwayADAge[AD]CD (P ≤ 0.01)Age[CD] (P ≤ 0.01)CD (P ≤ 0.05)Age[CD] (P ≤ 0.05)
Down-regulated
Staphylococcus aureus infectionN.S.N.S.N.S.N.S.N.S.N.S.
 Complement and coagulation cascadesN.S.N.S.N.S.N.S.N.S.N.S.
 ToxoplasmosisN.S.N.S.N.S.N.S.N.S.N.S.
 Mineral absorptionN.S.N.S.N.S.N.S.N.S.N.S.
 LegionellosisN.S.N.S.N.S.N.S.N.S.N.S.
 Proteoglycans in cancerN.S.N.S.N.S.N.S.N.S.N.S.
 MalariaN.S.N.S.N.S.N.S.N.S.N.S.
 PertussisN.S.N.S.N.S.N.S.N.S.N.S.
 Allograft rejectionN.S.N.S.N.S.N.S.N.S.N.S.
 Alzheimer’s disease1.39E-13N.S.N.S.N.S.N.S.9.07E-06
 Antigen processing and presentationN.S.N.S.N.S.N.S.N.S.N.S.
 AsthmaN.S.N.S.N.S.N.S.N.S.N.S.
 Axon guidanceN.S.1.14E-02N.S.N.S.N.S.N.S.
 Cardiac muscle contraction2.16E-07N.S.N.S.N.S.N.S.N.S.
 Citrate cycle (TCA cycle)1.84E-03N.S.N.S.N.S.N.S.N.S.
 Cysteine and methionine metabolism3.59E-02N.S.N.S.N.S.N.S.N.S.
 GABAergic synapse3.99E-05N.S.N.S.N.S.N.S.N.S.
 Huntington’s disease6.00E-15N.S.N.S.N.S.N.S.1.65E-03
 LeishmaniasisN.S.N.S.N.S.N.S.N.S.N.S.
 Morphine addiction3.26E-02N.S.N.S.N.S.N.S.N.S.
 NOD-like receptor signaling pathwayN.S.N.S.N.S.N.S.N.S.N.S.
 Nicotine addiction5.71E-04N.S.N.S.N.S.N.S.N.S.
 Nonalcoholic fatty liver disease4.77E-10N.S.N.S.N.S.N.S.1.59E-02
 Olfactory transductionN.S.N.S.N.S.N.S.4.52E-03N.S.
 Oxidative phosphorylation9.67E-20N.S.N.S.N.S.N.S.3.35E-07
 Parkinson’s disease2.12E-19N.S.N.S.N.S.N.S.1.36E-06
 Pathogenic Escherichia coli infection1.50E-02N.S.N.S.N.S.N.S.N.S.
 PhagosomeN.S.N.S.N.S.N.S.N.S.N.S.
 Proteasome4.86E-04N.S.N.S.N.S.N.S.1.57E-02
 Pyrimidine metabolismN.S.N.S.N.S.N.S.N.S.1.19E-01
 Retrograde endocannabinoid signaling7.59E-05N.S.N.S.N.S.N.S.N.S.
 RibosomeN.S.N.S.N.S.N.S.N.S.2.10E-01
 Synaptic vesicle cycle2.59E-08N.S.N.S.N.S.N.S.N.S.
 Systemic lupus erythematosusN.S.N.S.N.S.N.S.N.S.N.S.
Vibrio cholerae infection4.33E-02N.S.N.S.N.S.N.S.N.S.
Up-regulated
S. aureus infection2.12E-064.69E-11N.S.N.S.N.S.N.S.
 Complement and coagulation cascades1.91E-043.75E-07N.S.N.S.N.S.N.S.
 Toxoplasmosis7.92E-046.00E-03N.S.N.S.N.S.N.S.
 Mineral absorption2.67E-03N.S.N.S.2.40E-03N.S.4.94E-03
 Legionellosis7.73E-031.79E-02N.S.N.S.N.S.N.S.
 Proteoglycans in cancer2.74E-02N.S.N.S.N.S.N.S.N.S.
 Malaria3.04E-02N.S.N.S.N.S.N.S.N.S.
 Pertussis4.07E-024.39E-04N.S.N.S.N.S.N.S.
 Allograft rejectionN.S.2.74E-02N.S.N.S.N.S.N.S.
 Alzheimer’s diseaseN.S.N.S.N.S.N.S.N.S.N.S.
 Antigen processing and presentationN.S.2.86E-03N.S.N.S.N.S.N.S.
 AsthmaN.S.4.54E-02N.S.N.S.N.S.N.S.
 Axon guidanceN.S.N.S.N.S.N.S.N.S.N.S.
 Cardiac muscle contractionN.S.N.S.N.S.N.S.N.S.N.S.
 Citrate cycle (TCA cycle)N.S.N.S.N.S.N.S.N.S.N.S.
 Cysteine and methionine metabolismN.S.N.S.N.S.N.S.N.S.N.S.
 GABAergic synapseN.S.N.S.N.S.N.S.N.S.N.S.
 Huntington’s diseaseN.S.N.S.N.S.N.S.N.S.N.S.
 LeishmaniasisN.S.2.61E-04N.S.N.S.N.S.N.S.
 NOD-like receptor signaling pathwayN.S.2.46E-02N.S.N.S.N.S.N.S.
 Nicotine addictionN.S.N.S.N.S.N.S.N.S.N.S.
 Nonalcoholic fatty liver diseaseN.S.N.S.N.S.N.S.N.S.N.S.
 Olfactory transductionN.S.N.S.N.S.N.S.4.91E-02N.S.
 Oxidative phosphorylationN.S.N.S.N.S.N.S.N.S.N.S.
 Parkinson’s diseaseN.S.N.S.N.S.N.S.N.S.N.S.
 Pathogenic E. coli infectionN.S.N.S.N.S.N.S.N.S.N.S.
 PhagosomeN.S.1.31E-02N.S.N.S.N.S.N.S.
 ProteasomeN.S.N.S.N.S.N.S.N.S.N.S.
 Pyrimidine metabolismN.S.N.S.N.S.N.S.N.S.N.S.
 Retrograde endocannabinoid signalingN.S.N.S.N.S.N.S.N.S.N.S.
 RibosomeN.S.N.S.N.S.N.S.N.S.N.S.
 Synaptic vesicle cycleN.S.N.S.N.S.N.S.N.S.N.S.
 Systemic lupus erythematosusN.S.2.47E-05N.S.N.S.N.S.N.S.
V. cholerae infectionN.S.N.S.N.S.N.S.N.S.N.S.
  • In the case of aging, the pathways identified based on analyses of the Alzheimer’s disease (Age[AD]) dataset and the depression (Age[CD]) dataset are listed separately. For the depression and aging–depression sets, pathways enriched with expression significance cutoffs of P ≤ 0.01 and P ≤ 0.05 are both shown. Values shown are Holm–Bonferroni–corrected one-sided Fisher’s exact test P values, where the Holm–Bonferroni correction was applied to each dataset separately. Only P values ≤0.05 are listed. N.S., not significant; NOD, nucleotide oligomerization domain.