Table 6.
Top three pathways containing most unique biomarkers, as well as which biomarkers were not covered by the top three pathways (however were part of a PWM)
| HGNC Name Disorder | Patient Label; diagnosis possible? | (Yes, No, Direction) | Pathways in Top 3 (WikiPathways ID) [amount of covered biomarkers]* |
Not covered biomarkers (ChEBI IDs; corresponding names) |
|---|---|---|---|---|
| UPB1D | J | No |
Pyrimidine metabolism and related diseases (WP4225) [5] Amino acid metabolism (WP3925)# [3] Purine metabolism (WP4792) [3] |
4 (16283 18019 27596 30913; Cystine, Lysine, 3-Methyl-histidine, Pipecolic acid) |
| DPYD | A | Yes |
Amino acid metabolism (WP3925) [6] Biomarkers for pyrimidine metabolism disorders (WP4584) [5] Urea cycle and related diseases (WP4571)# [1] |
4 (17,553 18237 7274 15727; Phosphoethanolamine, Glutamic acid, Formiminoglutamic acid, Carnosine) |
| E | Direction |
Amino acid metabolism (WP3925) [5] Pyrimidine metabolism and related diseases (WP4225) [3] – |
4 (18237 35621 86498 16000; Glutamic acid, AABA, Hydroxylysine, Monoethanolamine) | |
| I | Yes |
Biomarkers for pyrimidine metabolism disorders (WP4584) [4] Purine metabolism (WP4792) [1] – |
2 (17261 70744; N-Aspartylglucosamine, Gly-pro) | |
| K | Yes |
Biomarkers for pyrimidine metabolism disorders (WP4584) [3] Urea cycle and related diseases (WP4571) [1] – |
1 (18237; Glutamic acid) | |
| ASL | F | Yes |
Biomarkers for urea cycle disorders (WP4583) [4] One-carbon metabolism and related pathways (WP3940) [3] Pyrimidine metabolism (WP4002) [1] |
4 (86498 15727 27596 85981; Hydroxylysine, Carnosine, 3-Methyl-histidine, Homocarnosine) |
| L | Yes |
Urea cycle and related diseases (WP4571) [4] Glycerophospholipid biosynthetic pathway (WP2533) [2] Amino acid metabolism (WP3925) [2] |
7 (18237 27596 85981 16283 17549 17261 17368; Glutamic acid, 3-Methyl-histidine, Homocarnosine, Cystine, Aminolevulinic acid, N-Aspartylglucosamine, Hypoxanthine) | |
| M | Yes |
Amino acid metabolism (WP3925) [14] Urea cycle and associated pathways (WP4595) [7] – |
9 (85981 15727 17261 16283 27596 18237 16000 18019 16865; Homocarnosine, Carnosine, N-Aspartylglucosamine, Cystine, 3-Methyl-histidine, Glutamic acid, Monoethanolamine, Lysine, GABA) | |
| N | Yes |
Amino acid metabolism (WP3925) [15] Urea cycle and associated pathways (WP4595) [7] – |
14 (17553 18237 85981 27596 15727 16865 17261 16000 37024 58148 18019 15611 27891 16283; Phosphoethanolamine, Glutamic acid, Homocarnosine, 3-Methyl-histidine, Carnosine, GABA, N-Aspartylglucosamine, Monoethanolamine, 2-Aminoadipic acid, Homocitrulline, Lysine, Sarcosine, S-sulfocysteine, Cystine) | |
| T | Yes |
Amino acid metabolism (WP3925) [12] Urea cycle and associated pathways (WP4595) [6] Vitamin B6-dependent and responsive disorders (WP4228) [3] |
11 (16000 27596 85981 17553 17261 18237 16283 17549 16865 16811 86498; Monoethanolamine, 3-Methyl-histidine, Homocarnosine, Phosphoethanolamine, N-Aspartylglucosamine, Glutamic acid, Cystine, Aminolevulinic acid, GABA, Methionine, Hydroxylysine) | |
| ASS1 | D | Yes |
Amino acid metabolism (WP3925) [7] Pyrimidine metabolism and related diseases (WP4225) [5] Vitamin B6-dependent and responsive disorders (WP4228) [2] |
3 (49015 7274 32682; Piperideine carboxylic acid, Formiminoglutamic acid, Arginine) |
| SLC25A15 | H | No |
Amino acid metabolism (WP3925) [16] Pyrimidine metabolism and related diseases (WP4225) [8] Biomarkers for urea cycle disorders (WP4583)# [3] |
21 (18019 27596 15611 16000 18323 18237 35621 37024 16283 86498 16865 15727 85981 16927 17261 17549 27891 70744 50599 7274 17553; Lysine, 3-Methyl-histidine, Sarcosine, Monoethanolamine, Anserine, Glutamic acid, AABA, 2-Aminoadipic acid, Cystine, Hydroxylysine, GABA, Carnosine, Homocarnosine, Saccharopine, N-Aspartylglucosamine, Aminolevulinic acid, S-sulfocysteine, Gly-pro, 1-Methyl-histidine, Formiminoglutamic acid, Phosphoethanolamine) |
| OTC | G | Direction |
Pyrimidine metabolism and related diseases (WP4225) [8] Alanine and aspartate metabolism (WP106) [2] Purine metabolism (WP4792) [2] |
7 (35621 58148 27596 37024 7274 16000 16414; AABA, Homocitrulline, 3-Methyl-histidine, 2-Aminoadipic acid, Formiminoglutamic acid, Monoethanolamine, Valine) |
| O | No |
Amino acid metabolism (WP3925) [15] Biomarkers for urea cycle disorders (WP4583) [7] One-carbon metabolism and related pathways (WP3940) [4] |
16 (18323 27891 50599 86498 27596 35621 18019 37024 15727 18237 16283 17261 7274 16865 85981 17568; Anserine, S-sulfocysteine, 1-Methyl-histidine, Hydroxylysine, 3-Methyl-histidine, AABA, Lysine, 2-Aminoadipic acid, Carnosine, Glutamic acid, Cystine, N-Aspartylglucosamine, Formiminoglutamic acid, GABA, Homocarnosine, Uracil) | |
| R | Direction |
Amino acid metabolism (WP3925) [16] Pyrimidine metabolism and related diseases (WP4225) [7] Biomarkers for urea cycle disorders (WP4583) [3] |
17 (17553 16000 18019 15727 16865 27596 18237 16283 16811 17261 86498 85981 27891 17549 35621 15611 37024; Phosphoethanolamine, Monoethanolamine, Lysine, Carnosine, GABA, 3-Methyl-histidine, Glutamic acid, Cystine, Methionine, N-Aspartylglucosamine, Hydroxylysine, Homocarnosine, S-sulfocysteine, Aminolevulinic acid, AABA, Sarcosine, 2-Aminoadipic acid) | |
| S | Direction |
Amino acid metabolism (WP3925) [15] Pyrimidine metabolism and related diseases (WP4225) [6] Glycerolipids and glycerophospholipids (WP4722)# [2] |
13 (85981 15727 16811 27596 16865 18019 16283 57472 86498 17261 18237 35621 17549; Homocarnosine, Carnosine, Methionine, 3-Methyl-histidine, GABA, Lysine, Cystine, Argininosuccinate, Hydroxylysine, N-Aspartylglucosamine, Glutamic acid, AABA, Aminolevulinic acid) |
# indicates different pathways cover the same amount of unique metabolites leading to a manual selection of the most relevant pathway
* : – indicates no third pathway was selected