Table 2.
Genes with significant changes in expression as identified by OpWise methods and by SAM.
| dvSalt30 | ecox | shHeat5 | shCold5 | |||||
| Method | #Genes | %Agree | #Genes | %Agree | #Genes | %Agree | #Genes | %Agree |
| 1-gene (OpWise) | 220 | 100% | 1062 | 98% | 1002 | 97% | 187 | 100% |
| operon-wise | 401 | 99% | 1318 | 100% | 1284 | 99% | 374 | 100% |
| no-bias | 1090 | 90% | 1269 | 98% | 3020 | 87% | 3063 | 70% |
| SAM | 852 | 94% | 957 | 99% | 3348 | 83% | 3258 | 68% |
For OpWise, genes were selected if the two-tailed confidence was 95% or higher (P(μi > 0) < 0.025 or P(μi < 0) > 0.975). For SAM, genes were selected if the false discovery rate was 5% or lower. For each method and for each data set, we report how many genes were selected as significant changers and what percentage of the operon pairs that contain those genes changed in the same direction. This "agreement" should be 100% for perfect microarray data and perfect operon predictions and 50% for random data.