Skip to main content
. Author manuscript; available in PMC: 2023 Feb 1.
Published in final edited form as: J Parkinsons Dis. 2022;12(8):2441–2452. doi: 10.3233/JPD-223500

Table 3.

Differential predicted Metacyc pathways abundance associated with PD compared to two different control groups (total and household only)

Metacyc pathways Main Analysisa
(N=170)
 Sensitivity
Analysis 1b
(N=153)
 Sensitivity
Analysis 2c
(N=100)
 Sensitivity
Analysis 3d
(N=170)
Log2FCe Adj P Log2FCe Adj P Log2FCe Adj p Log2FCe Adj p
Allantoin degradation to glyoxylate III 1.06 0.0000 1.14 0.0005 0.39 0.0500 0.75 0.0000
Superpathway of (R,R)-butanediol biosynthesis 1.09 0.0064 1.37 0.0011 0.37 0.2696 0.78 0.0002
Superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 0.70 0.0064 0.68 0.0189 0.57 0.0031 0.55 0.0001
Glucose and glucose-1-phosphate degradation 1.00 0.0139 1.02 0.0189 0.75 0.0096 0.75 0.0005
1,4-dihydroxy-2-naphthoate biosynthesis I 0.90 0.0155 0.91 0.0266 0.81 0.0048 0.68 0.0008
Superpathway of phylloquinol biosynthesis 0.88 0.0157 0.88 0.0271 0.80 0.0049 0.66 0.0009
NAD salvage pathway II 0.76 0.0250 0.59 0.0717 0.48 0.0819 0.55 0.0022
4-hydroxyphenylacetate degradation 1.98 0.0265 3.04 0.0016 0.75 0.3603 1.72 0.0007
L-arginine degradation II (AST pathway) 1.41 0.0265 1.41 0.0408 0.32 0.6855 1.03 0.0043
D-glucarate degradation I 0.68 0.0265 0.71 0.0345 0.34 0.1477 0.50 0.0030
Superpathway of demethylmenaquinol-8 biosynthesis 0.72 0.0265 0.74 0.0345 0.70 0.0065 0.56 0.0023
Superpathway of menaquinol-11 biosynthesis 0.68 0.0265 0.71 0.0345 0.65 0.0085 0.53 0.0025
Superpathway of menaquinol-12 biosynthesis 0.68 0.0265 0.71 0.0345 0.65 0.0085 0.53 0.0025
Superpathway of menaquinol-13 biosynthesis 0.68 0.0265 0.71 0.0345 0.65 0.0085 0.53 0.0025
Gondoate biosynthesis (anaerobic) −0.15 0.0265 −0.17 0.0317 −0.07 0.1253 −0.09 0.0076
Superpathway of L-aspartate and L-asparagine biosynthesis −0.16 0.0282 −0.19 0.0281 −0.07 0.1338 −0.09 0.0134
Fatty acid β-oxidation I 0.95 0.0282 1.04 0.0345 0.10 0.8613 0.70 0.0060
Superpathway of menaquinol-8 biosynthesis I 0.65 0.0282 0.68 0.0345 0.63 0.0092 0.51 0.0031
Superpathway of menaquinol-7 biosynthesis 0.65 0.0282 0.68 0.0345 0.63 0.0092 0.51 0.0031
Norspermidine biosynthesis 2.10 0.0282 2.27 0.0345 1.18 0.1868 1.52 0.0079
Polymyxin resistance 1.27 0.0282 1.13 0.0601 0.65 0.2349 0.93 0.0060
Cis-vaccenate biosynthesis −0.14 0.0310 −0.18 0.0283 −0.07 0.1220 −0.08 0.0196
Allantoin degradation IV (anaerobic) 1.60 0.0311 1.64 0.0556 0.82 0.2761 1.16 0.0077
Adenosylcobalamin salvage from cobinamide I −0.20 0.0340 −0.24 0.0345 −0.13 0.0561 −0.14 0.0153
Glycogen biosynthesis I (from ADP-D-Glucose) −0.20 0.0340 −0.24 0.0336 −0.13 0.0229 −0.12 0.0175
Adenosylcobalamin biosynthesis from cobyrinate a,c-diamide I −0.21 0.0340 −0.24 0.0345 −0.13 0.0498 −0.14 0.0157
Nitrate reduction VI (assimilatory) −0.46 0.0340 −0.57 0.0271 −0.36 0.0277 −0.34 0.0086
Adenosylcobalamin salvage from cobinamide II −0.21 0.0340 −0.24 0.0345 −0.13 0.0525 −0.13 0.0162
Arginine, ornithine and proline interconversion 0.47 0.0354 0.35 0.1510 0.12 0.5778 0.34 0.0114
Superpathway of 2,3-butanediol biosynthesis 0.77 0.0368 1.20 0.0021 0.30 0.3243 0.58 0.0068
Formaldehyde assimilation II (RuMP Cycle) 0.63 0.0381 0.46 0.1757 0.14 0.6759 0.46 0.0134
Mevalonate pathway I 0.93 0.0381 0.98 0.0556 0.79 0.0691 0.68 0.0125
NAD salvage pathway I −0.16 0.0381 −0.17 0.0556 −0.08 0.1062 −0.09 0.0252
Superpathway of N-acetylneuraminate degradation 0.25 0.0433 0.27 0.0561 0.19 0.1157 0.22 0.0047
Superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 0.88 0.0450 0.93 0.0556 0.77 0.0706 0.65 0.0154
a

Included both community controls and population controls; adjusted for sex, race, age, and sequencing platform. DESeq2 was used to perform the analysis.

b

Included both community controls and population controls; adjusted for sex, race, age, and sequencing platform and constipation status. DESeq2 was used to perform the analysis.

c

Included household controls only: PD patient and household control pair was treated as random effect. Adjusted for sex, race, age, and sequencing platform. MaAsLin2 was used to perform the analysis.

d

Included both community controls and population controls; adjusted for sex, race, age, and sequencing platform. MaAsLin2 was used to perform the analysis.

e

Coefficient indicates the difference in the log-transformed relative abundances between PD and Control. Log2FC, Log2 fold change; Adj, adjusted.