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Table 2 Genes with significant changes in expression as identified by OpWise methods and by SAM.

From: OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

 

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%

  1. For OpWise, genes were selected if the two-tailed confidence was 95% or higher (P(μ i > 0) < 0.025 or P(μ i < 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.