Table 3 Overview of biomarker data per patient, including the number of altered biomarkers and coverage thereof in pathways models, as well as theoretical biomarker clustering information for the investigated phenotypes and corresponding genes
From: Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations
HGNC Name Disorder | Patient Label | Biomarkers with reference data | Altered biomarkers | Amount of Biomarkers not in any pathway (ChEBI IDs; corresponding names) | Total amount of relevant pathways (First pathway biomarker coverage) | Closest related gene(s) through clustering (additional biomarkers)* |
|---|---|---|---|---|---|---|
UPB1D | J | 65 | 15 | 1 (27,596; 3-Methyl-histidine) | 37 (5) | DPYS/UPB1 (8) |
DPYD | A | 61 | 16 | – | 47 (6) | DPYD (13) |
E | 54 | 12 | 2 (35,621, 86,498; AABA, Hydroxylysine) | 41 (5) | DPYD (9) | |
I | 60 | 7 | 2 (17,261, 70,744; N-Aspartylglucosamine, Gly-pro) | 9 (4) | – (4) | |
K | 45 | 5 | – | 10 (3) | DPYD (3) | |
ASL | F | 52 | 12 | 2 (86,498, 27,596; Hydroxylysine, 3-Methyl-histidine) | 23 (4) | – (7) |
L | 50 | 15 | 2 (27,596, 17,261; 3-Methyl-histidine, N-Aspartylglucosamine) | 31 (4) | – (10) | |
M | 56 | 30 | 2 (17,261, 27,596; N-Aspartylglucosamine, 3-Methyl-histidine) | 75 (14) | – (25) | |
N | 61 | 36 | 2 (27,596, 17,261; 3-Methyl-histidine, N-Aspartylglucosamine) | 76 (15) | – (28) | |
T | 58 | 32 | 3 (27,596, 17,261, 86,498; 3-Methyl-histidine, N-Aspartylglucosamine, Hydroxylysine) | 77 (12) | – (28) | |
ASS1 | D | 59 | 16 | 1 (49,015; Piperideine carboxylic acid) | 46 (7) | – (12) |
SLC25A15 | H | 61 | 48 | 6 (27,596, 35,621, 86,498, 17,261, 70,744, 50,599; 3-Methyl-histidine, AABA, Hydroxylysine, N-Aspartylglucosamine, Gly-pro, 1-Methyl-histidine) | 77 (16) | – (40) |
OTC | G | 67 | 19 | 2 (35,621, 27,596; AABA, 3-Methyl-histidine) | 26 (8) | – (10) |
O | 55 | 42 | 5 (50,599, 86,498, 27,596, 35,621, 17,261; 1-Methyl-histidine, Hydroxylysine, 3-Methyl-histidine, AABA, N-Aspartylglucosamine) | 77 (15) | – (37) | |
R | 62 | 43 | 4 (27,596, 17,261, 86,498, 35,621; 3-Methyl-histidine, N-Aspartylglucosamine, Hydroxylysine, AABA) | 78 (16) | – (35) | |
S | 62 | 36 | 4 (27,596, 86,498, 17,261, 35,621; 3-Methyl-histidine, Hydroxylysine, N-Aspartylglucosamine, AABA) | 74 (15) | – (29) |