Table 1 Percentage of correct entries in the inferred truth tables for synthetic networks for E. coli and S. cerevisiae.
From: IRIS: a method for reverse engineering of regulatory relations in gene networks
E. Coli | |||||
|---|---|---|---|---|---|
| Â | Â | Â | True Table vs IRIS Inferred TT | ||
Regulated Gene | Regulator Genes | TT Size | Correct | Incorrect | Undefined |
glcD | glcC arcA | 4 | 4 | 0 | 0 |
focA | arcA crp | 4 | 4 | 0 | 0 |
rpoH | crp | 2 | 2 | 0 | 0 |
tdc | crp | 2 | 2 | 0 | 0 |
lacZ | crp lacI | 4 | 4 | 0 | 0 |
Total | 16 | 16 | 0 | 0 | |
Percentage | 100% | 0% | 0% | ||
S. cerevisiae | |||||
| Â | Â | Â | True Table vs IRIS Inferred TT | ||
Regulated Gene | Regulator Genes | TT Size | Correct | Incorrect | Undefined |
CLN2 | SSL1 | 2 | 2 | 0 | 0 |
CDC28 | SSL1 | 2 | 2 | 0 | 0 |
NOT3 | SSL1 | 2 | 2 | 0 | 0 |
FIT2 | SSL1 PDR11 | 4 | 4 | 0 | 0 |
CDC6 | PDR11 | 2 | 2 | 0 | 0 |
CEF1 | PDR11 | 2 | 1 | 1 | 0 |
LEU2 | PDR11 | 2 | 2 | 0 | 0 |
CLB6 | PDR11 | 2 | 2 | 0 | 0 |
DAL80_GZF3 | PDR11 | 2 | 2 | 0 | 0 |
A2 | PDR11 IPT1 | 4 | 4 | 0 | 0 |
Total | 24 | 23 | 1 | 0 | |
Percentage | 95.83% | 4.17% | 0% | ||
- Truth tables (TTs) were computed using the data set with the maximum biological noise level (0.50). "TT Size" reports the number of possible state assignments for the regulator genes. Note that the value for the i-th regulated gene is
, where |Ri| is the number of regulators and each gene can be in two states. We distinguish the number of correct/incorrect/undefined inferred states for each regulatory relation and compute these as percentages of the total number of states.
, where |Ri| is the number of regulators and each gene can be in two states. We distinguish the number of correct/incorrect/undefined inferred states for each regulatory relation and compute these as percentages of the total number of states.