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Table 1 Comparison of yeast metabolic models

From: Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

  Yeast 5 Yeast 4 a iMM904bs b iND750 c
Model description     
Number of metabolites 1655 1481 1228 1061
Number of reactions 2110 2030 1575 1266
Number of genes 918 924 904 750
Number of dubious genesd 0 4 17 17
Blocked reactionse 38% 26% 31% 41%
Viability analysis     
ensitivityf 97% 95% 93% 96%
Specificityg 47% 44% 57% 43%
Positive predictive valueh 86% 85% 89% 87%
Negative predictive valuei 84% 73% 69% 77%
Geometric meanj 46% 42% 53% 41%
Auxotrophy analysis     
Auxotroph-inducing genes includedk 70 73 73 69
Correct auxotroph predictions 73% 66% 69% 58%
Incorrectly predicted as viable in minimal media 24% 30% 27% 39%
Incorrectly predicted as inviable in supplemented media 3% 4% 4% 3%
Epistatic interaction analysis l     
Epistatic interations (% of pairwise genes) 16% - 15% 21%
Total number of epistatic interactions 65,730 - 63,176 57,808
Average Additional Interactions per additional genem 196.46 - 34.63 -
  1. ayeast 4: [16].
  2. biMM904bs: [29].
  3. ciND750: [9].
  4. ddubious genes are ORFs annotated as "dubious" (809 ORFs) or "uncharacterized" (857 ORFs) in SGD.
  5. eblocked reactions cannot carry flux.
  6. fTrue positive/(true positive + false negative).
  7. gTrue negative/(true negative + false positive).
  8. hTrue positive/(true positive + false positive).
  9. iTrue negative/(true negative + false negative).
  10. jsee [10] for discussion of applying geometric mean
  11. ksee Additional file 8: Table S3 and Additional file 9: Table S4 for list of essential genes and auxotroph-inducing genes.
  12. lAt 50%x50% flux reductions. See Additional file 10: Table S5 for other restriction levels.
  13. m number of interactions/number of genes, compared to iND750 as base case.