TABLE 3.
Elevated metabolic pathways
| Pathway | Class | Coefficient a | SEM | Prevalence b | p | q |
|---|---|---|---|---|---|---|
| COA PWY: coenzyme A biosynthesis I: prokaryotic | Biosynthesis | 0.257 | 0.052 | 36 | 0.00002 | 0.01318 |
| GLYCOGENSYNTH PWY: glycogen biosynthesis I: from ADP D Glucose | Biosynthesis | 0.751 | 0.142 | 36 | 0.00001 | 0.01318 |
| PWY 4242: pantothenate and coenzyme A biosynthesis III | Biosynthesis | 0.285 | 0.056 | 36 | 0.00001 | 0.01318 |
| PWY 5100: pyruvate fermentation to acetate and lactate II | Degradation/use | 0.747 | 0.149 | 36 | 0.00002 | 0.01318 |
| PWY 6471: peptidoglycan biosynthesis IV: Enterococcus faecium | Biosynthesis | 1.265 | 0.249 | 36 | 0.00001 | 0.01318 |
| ARO PWY: chorismate biosynthesis I | Biosynthesis | 0.304 | 0.068 | 36 | 0.00009 | 0.01343 |
| BRANCHED CHAIN AA SYN PWY: superpathway of branched chain amino acid biosynthesis | Biosynthesis | 0.268 | 0.063 | 36 | 0.00017 | 0.01343 |
| COMPLETE ARO PWY: superpathway of aromatic amino acid biosynthesis | Biosynthesis | 0.309 | 0.070 | 36 | 0.00009 | 0.01343 |
| HSERMETANA PWY: L methionine biosynthesis III | Biosynthesis | 0.472 | 0.099 | 36 | 0.00003 | 0.01343 |
| LACTOSECAT PWY: lactose and galactose degradation I | Degradation/use | 1.592 | 0.379 | 36 | 0.00018 | 0.01343 |
| PWY 5097: L lysine biosynthesis VI | Biosynthesis | 0.216 | 0.051 | 36 | 0.00017 | 0.01343 |
| PWY 5103: L isoleucine biosynthesis III | Biosynthesis | 0.311 | 0.070 | 36 | 0.00009 | 0.01343 |
| PWY 6270: isoprene biosynthesis I | Biosynthesis | 0.562 | 0.121 | 36 | 0.00005 | 0.01343 |
| PWY 7221: guanosine ribonucleotides de novo biosynthesis | Biosynthesis | 0.237 | 0.051 | 36 | 0.00005 | 0.01343 |
| PWY 724: superpathway of L lysine: L threonine and L methionine biosynthesis II | Biosynthesis | 0.262 | 0.058 | 36 | 0.00006 | 0.01343 |
| PWY 7357: thiamine phosphate formation from pyrithiamine and oxythiamine: yeast | Biosynthesis | 0.419 | 0.093 | 36 | 0.00008 | 0.01343 |
| PWY 7560: methylerythritol phosphate pathway II | Biosynthesis | 0.597 | 0.129 | 36 | 0.00005 | 0.01343 |
| GLUTORN PWY: L ornithine biosynthesis I | Biosynthesis | 0.369 | 0.091 | 36 | 0.00028 | 0.01710 |
| METH ACETATE PWY: methanogenesis from acetate | Energy generation | 1.690 | 0.421 | 36 | 0.00031 | 0.01780 |
| NONOXIPENT PWY: pentose phosphate pathway: non oxidative branch: I | Energy generation | 0.606 | 0.154 | 36 | 0.00038 | 0.02008 |
| PWY 6527: stachyose degradation | Degradation/use | 0.677 | 0.176 | 36 | 0.00051 | 0.02400 |
| P4 PWY: superpathway of L lysine: L threonine and L methionine biosynthesis I | Biosynthesis | 1.269 | 0.331 | 36 | 0.00051 | 0.02401 |
| CALVIN PWY: Calvin Benson Bassham cycle | Biosynthesis | 0.358 | 0.094 | 36 | 0.00057 | 0.02470 |
| PWY 5188: tetrapyrrole biosynthesis I: from glutamate | Biosynthesis | 0.792 | 0.209 | 36 | 0.00058 | 0.02470 |
| PWY 6121: 5 aminoimidazole ribonucleotide biosynthesis I | Biosynthesis | 0.223 | 0.059 | 36 | 0.00058 | 0.02470 |
| DAPLYSINESYN PWY: L lysine biosynthesis I | Biosynthesis | 1.041 | 0.283 | 36 | 0.00080 | 0.02734 |
| PWY 6163: chorismate biosynthesis from 3 dehydroquinate | Biosynthesis | 0.255 | 0.069 | 36 | 0.00078 | 0.02734 |
| PWY 6606: guanosine nucleotides degradation II | Degradation/use | 0.869 | 0.236 | 36 | 0.00080 | 0.02734 |
| SER GLYSYN PWY: superpathway of L serine and glycine biosynthesis I | Biosynthesis | 0.439 | 0.118 | 36 | 0.00074 | 0.02734 |
| ARGININE SYN4 PWY: L ornithine biosynthesis II | Biosynthesis | −3.235 | 0.636 | 32 | 0.00001 | 0.01318 |
| HISDEG PWY: L histidine degradation I | Degradation/use | −1.876 | 0.383 | 36 | 0.00002 | 0.01318 |
| PWY 1269: CMP 3 deoxy D manno octulosonate biosynthesis | Biosynthesis | −1.837 | 0.373 | 36 | 0.00002 | 0.01318 |
| PWY 5973: cis vaccenate biosynthesis | Biosynthesis | −1.440 | 0.288 | 36 | 0.00002 | 0.01318 |
| PWY 7663: gondoate biosynthesis: anaerobic | Biosynthesis | −1.556 | 0.300 | 36 | 0.00001 | 0.01318 |
| CITRULBIO PWY: L citrulline biosynthesis | Biosynthesis | −2.367 | 0.540 | 35 | 0.00011 | 0.01343 |
| POLYISOPRENSYN PWY: polyisoprenoid biosynthesis: E: coli | Biosynthesis | −1.875 | 0.443 | 36 | 0.00017 | 0.01343 |
| PWY 4984: urea cycle | Degradation/use | −2.402 | 0.547 | 35 | 0.00010 | 0.01343 |
| PWY 5030: L histidine degradation III | Degradation/use | −1.743 | 0.381 | 36 | 0.00006 | 0.01343 |
| PWY 5505: L glutamate and L glutamine biosynthesis | Biosynthesis | −2.094 | 0.483 | 35 | 0.00012 | 0.01343 |
| PWY0 845: superpathway of pyridoxal 5: phosphate biosynthesis and salvage | Biosynthesis | −2.621 | 0.560 | 33 | 0.00004 | 0.01343 |
| PYRIDOXSYN PWY: pyridoxal 5: phosphate biosynthesis I | Biosynthesis | −2.892 | 0.602 | 33 | 0.00003 | 0.01343 |
| PWY 6859: all trans farnesol biosynthesis | Biosynthesis | −2.037 | 0.493 | 36 | 0.00022 | 0.01441 |
| PWY 7539: 6 hydroxymethyl dihydropterin diphosphate biosynthesis III: Chlamydia | Biosynthesis | −1.551 | 0.376 | 36 | 0.00023 | 0.01461 |
| PWY 5104: L isoleucine biosynthesis IV | Biosynthesis | −2.218 | 0.546 | 33 | 0.00027 | 0.01663 |
| PWY 6147: 6 hydroxymethyl dihydropterin diphosphate biosynthesis I | Biosynthesis | −1.529 | 0.380 | 36 | 0.00030 | 0.01751 |
| PWY 7332: superpathway of UDP N acetylglucosamine derived O antigen building blocks biosynthesis | Biosynthesis | −2.241 | 0.557 | 17 | 0.00030 | 0.01751 |
| PWY 7392: taxadiene biosynthesis: engineered | Biosynthesis | −1.781 | 0.448 | 36 | 0.00035 | 0.01877 |
| TCA: TCA cycle I: prokaryotic | Energy generation | −0.855 | 0.218 | 36 | 0.00040 | 0.02066 |
| NAD BIOSYNTHESIS II: NAD salvage pathway III: to nicotinamide riboside | Biosynthesis | −2.145 | 0.582 | 33 | 0.00079 | 0.02734 |
| PWY 7282: 4 amino 2 methyl 5 diphosphomethylpyrimidine biosynthesis II | Biosynthesis | −1.428 | 0.388 | 35 | 0.00080 | 0.02734 |
a
Positive coefficients indicate an elevated pathway in the NAFLD group, and negative coefficients indicate a reduced pathway in the NAFLD group.
b
Prevalence indicates the number of samples in which this particular pathway was detected.