Table 4 |
|||||||
|
Comparison of genes identified as differentially expressed in mac1Δ |
|||||||
|
Gene |
ORF |
Loguinov et al. (this work) (0.0001) |
Hughes et al. [18] (0.0001) |
Churchill and Sapir [20] (0.9999) |
Newton et al. [19] (0.9999) |
2FC |
Reference |
|
|
|||||||
|
FTH1 |
YBR207W |
+ |
+ |
+ |
+ |
+ |
[67] |
|
PCA1 |
YBR295W |
+ |
a |
+ |
+ |
a |
[68] |
|
AKR1 |
YDR264C |
+ |
a |
+ |
+ |
a |
[69] |
|
CCC2 |
YDR270W |
+ |
+ |
+ |
+ |
+ |
[67] |
|
FIT1 |
YDR534C |
+ |
a |
+ |
+ |
+ |
[70] |
|
SIT1 |
YEL065W |
+ |
+ |
+ |
+ |
+ |
[70] |
|
FTR1 |
YER145C |
+ |
+ |
+ |
+ |
+ |
[67] |
|
FET5 |
YFL041W |
+ |
a |
+ |
+ |
[71] |
|
|
YFR055W* |
- |
b |
b |
b |
b |
[72] |
|
|
CTT1 |
YGR088W* |
- |
b |
b |
b |
b |
[33] |
|
VMR1 |
YHL035C |
+ |
+ |
+ |
+ |
+ |
[69] |
|
ARN1 |
YHL040C |
+ |
+ |
+ |
+ |
+ |
[70] |
|
ARN2 |
YHL047C |
+ |
+ |
+ |
+ |
+ |
[70] |
|
FRE2 |
YKL220C |
+ |
a |
+ |
+ |
+ |
[67] |
|
MRS4 |
YKR052C* |
+ |
a |
a |
a |
a |
[73] |
|
FRE6 |
YLL051C |
+ |
a |
+ |
+ |
a |
[74] |
|
SMF3 |
YLR034C* |
+ |
a |
a |
a |
a |
[75] |
|
TIS11 |
YLR136C |
+ |
a |
+ |
+ |
a |
[76] |
|
HMX1 |
YLR205C |
+ |
+ |
+ |
+ |
+ |
[77] |
|
FRE1 |
YLR214W |
+ |
+ |
+ |
+ |
+ |
[67] |
|
MAC1 |
YMR021C |
- |
a |
- |
- |
- |
[33] |
|
FET3 |
YMR058W |
+ |
+ |
+ |
+ |
+ |
[67] |
|
ATX1 |
YNL259C |
+ |
a |
+ |
+ |
a |
[78] |
|
BIO5 |
YNR056C |
+ |
a |
+ |
+ |
+ |
[69] |
|
FRE4 |
YNR060W |
+ |
a |
+ |
+ |
+ |
[74] |
|
ARN4 |
YOL158C |
+ |
+ |
+ |
+ |
+ |
[70] |
|
FRE3 |
YOR381W |
+ |
+ |
+ |
+ |
+ |
[74] |
|
FIT2 |
YOR382W |
+ |
+ |
+ |
+ |
+ |
[79] |
|
FIT3 |
YOR383C |
+ |
+ |
+ |
+ |
+ |
[79] |
|
FRE5 |
YOR384W |
+ |
+ |
+ |
+ |
+ |
[74] |
|
|
|||||||
|
The performance of each method (except Chen et al. [17]) at equivalently high stringency levels is presented for selected genes likely to be differentially expressed in mac1Δ as described in text. For Sapir and Churchill [20], the cut-off (0.9999) corresponds to posterior probability of being differentially expressed and for Newton et al. [19], the cut-off 0.9999 is posterior probability of true differential expression. For this work, 0.0001 is a cut-off for q-values. For Hughes et al. [18], 0.0001 is a cut-off for p-values. 2FC is indicates two-fold change approach. A (+) sign indicates that a gene was identified as up-regulated by a method at this level of stringency while a (-) sign indicates that it was identified as down-regulated. Genes not identified by one method that were identified by other methods are indicated by a (+) or b (-) in the appropriate column. Genes identified only by this work are asterisked. |
|||||||
|
Loguinov et al. Genome Biology 2004 5:R18 doi:10.1186/gb-2004-5-3-r18 |
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