Table 1

Comparison of yeast metabolic models
    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
  Sensitivityf 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 analysisl
  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 -

ayeast 4: [16].

biMM904bs: [29].

ciND750: [9].

ddubious genes are ORFs annotated as "dubious" (809 ORFs) or "uncharacterized" (857 ORFs) in SGD.

eblocked reactions cannot carry flux.

fTrue positive/(true positive + false negative).

gTrue negative/(true negative + false positive).

hTrue positive/(true positive + false positive).

iTrue negative/(true negative + false negative).

jsee [10] for discussion of applying geometric mean

ksee Additional file 8: Table S3 and Additional file 9: Table S4 for list of essential genes and auxotroph-inducing genes.

lAt 50%x50% flux reductions. See Additional file 10: Table S5 for other restriction levels.

m number of interactions/number of genes, compared to iND750 as base case.

Heavner et al.

Heavner et al. BMC Systems Biology 2012 6:55   doi:10.1186/1752-0509-6-55

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