Table 4.
Using EMMs to compare the annotation opportunities of PubChem against the KEGG database.(A) Experimental data for different datasets (repeated for convenience). (B) Number of matched masses and candidate chemicals found using EMMF that are reported in KEGG. (C) Number of matched masses and candidate chemicals found using EMMF reported in PubChem but not in KEGG. (D) Lower-bounds on discovery of biologically relevant matched masses and candidate chemicals when using PubChem over KEGG.
| Biological Sample | (A) Experimental Data |
(B) In EMM And in KEGG |
(C) In EMM And PubChem, And Not in KEGG |
(D) Lower-Bound Fold Increase of Pubchem over KEGG |
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|---|---|---|---|---|---|---|---|---|
| Dataset | Number of Measured Masses | Number of Matched Masses | Number of Candidate Chemical IDs | Number of Matched Masses | Number of Candidate Chemical IDs | Number of Matched Masses | Number of Candidate Chemical IDs | |
| CHO cell | HilNeg | 2502 | 56 | 93 | 118 | 200 | 2.11 | 2.15 |
| HilPos | 3856 | 26 | 39 | 106 | 148 | 4.08 | 3.79 | |
| SynNeg | 5336 | 88 | 122 | 205 | 283 | 2.33 | 2.32 | |
| gut microbiota | Neg | 1651 | 25 | 47 | 52 | 113 | 2.08 | 2.40 |
| Pos | 1657 | 23 | 28 | 61 | 93 | 2.65 | 3.32 | |
| Average | 2.65 | 2.80 | ||||||