Table 1.
Dataset description of used dataset for the TK, HMC, and SCD studies
| Study name | TK | HMC | SCD | TK-None |
|---|---|---|---|---|
| Summary stats cut-off | 1.03 × 10−10 | 1.79 × 10-7 | None | None |
| Sample size | 7,824 | 614 | 651 | 7,824 |
| SNP-Metabolite name pairs (unique SNP - unique metabolites) |
336 (218-186) |
6 465 (3 192-100) |
3 139 070 208 (24 523 986-128) |
1 236 909 025 (2 617 408–486) |
| Enzyme Gene-Metabolite pairs with KEGG IDs: PathQuant input (unique genes - unique metabolites)[gene - metabolite proportion mapped∗] |
74 (43–56)[20%–30%] |
68 (32-20)[1–20%] |
209 645 290 (3875-118)[16%–92%] |
46 779 684 (3815-177)[0.14%–36%] |
| Pairs’ SRD annotations within KEGG Overview Graph (unique genes - unique metabolites∗∗)[gene - metabolite proportion mapped∗] |
SRD: 38 Inf: 2 NA: 34 (27–33)[63%–59%] |
SRD: 38 Inf: 4 NA: 26 (13 - 8)[40%–40%] |
SRD: 82 145 Inf: 38 980 NA: 336 125 (1275 - 95)[33%–81%] |
SRD: 86 219 Inf: 55 822 NA: 533 214 (1257 - 113)[33%–64%] |
Line 1: Dataset label for TK, HMC, and SCD studies and the TK dataset without p values cut-off (TK-None). Line 2: Maximum p value cut-off. Line 3: Maximum number of samples available for the mGWAS study. Line 4: Number of SNP-metabolites pairs. Line 5: Number of gene coding for enzyme-metabolite pairs for which KEGG IDs have been obtained. Line 6: Number of SRD annotation within map hsa01100 (KEGG overview graph) categorized in three categories. Lines 4, 5, and 6 have the count of unique genes and metabolites involved in pairs between parenthesis. ∗: the proportion of genes and metabolites mapped from the previous line is indicated between brackets. ∗∗: the number of unique genes and metabolites are ignoring NA values. Abbreviations: ID = Identifier; SNP = Single-nucleotide polymorphism; SRD = Shortest Reactional Distance; Inf = Infinite value; NA = Not available, a missing annotation.