Table 3 |
|||||||||||
|
Candidate differentially-expressed genes |
|||||||||||
|
RN |
ORF Name |
Synonyms |
CIN |
log2(Cy3) |
log2(Cy5/Cy3) |
RSE |
SR |
p |
p' |
p'' |
q |
|
|
|||||||||||
|
Up-regulated genes |
|||||||||||
|
1 |
YBR207W |
427 |
-0.62 |
1.06 |
0.14 |
7.30 |
3.30E-13 |
2.00E-09 |
2.01E-11 |
1.11E-10 |
|
|
2 |
YBR295W |
PCA1, PAY2 |
515 |
-2.30 |
0.83 |
0.16 |
5.26 |
1.50E-07 |
9.13E-04 |
9.18E-06 |
2.47E-05 |
|
3 |
YDR264C |
AKR1 |
1186 |
0.10 |
0.87 |
0.17 |
5.22 |
1.81E-07 |
1.10E-03 |
1.11E-05 |
2.90E-05 |
|
4 |
YDR270W |
CCC2 |
1192 |
-2.98 |
1.19 |
0.21 |
5.75 |
9.09E-09 |
5.52E-05 |
5.54E-07 |
1.62E-06 |
|
5 |
YDR476C |
1394 |
-1.87 |
0.84 |
0.14 |
6.08 |
1.24E-09 |
7.51E-06 |
7.55E-08 |
2.78E-07 |
|
|
6 |
YDR534C |
1452 |
-3.83 |
3.43 |
0.25 |
13.66 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
7 |
YEL065W |
SIT1 |
1528 |
-0.60 |
2.46 |
0.15 |
16.89 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
8 |
YER145C |
FTR1 |
1692 |
-0.49 |
2.25 |
0.15 |
15.11 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
9 |
YFL041W |
FET5 |
1778 |
-0.84 |
0.94 |
0.14 |
6.76 |
1.54E-11 |
9.32E-08 |
9.37E-10 |
4.05E-09 |
|
10 |
YGL015C |
1879 |
-3.40 |
1.04 |
0.23 |
4.53 |
6.07E-06 |
3.69E-02 |
3.71E-04 |
7.23E-04 |
|
|
11 |
YGL039W |
1903 |
-0.68 |
1.01 |
0.14 |
7.06 |
1.80E-12 |
1.10E-08 |
1.10E-10 |
5.76E-10 |
|
|
12 |
YGR065C |
2189 |
-0.19 |
0.76 |
0.16 |
4.82 |
1.49E-06 |
9.01E-03 |
9.06E-05 |
1.80E-04 |
|
|
13 |
YHL035C |
2453 |
-2.20 |
1.70 |
0.15 |
11.07 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
14 |
YHL040C |
ARN1 |
2458 |
-2.38 |
2.45 |
0.16 |
14.95 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
15 |
YHL047C |
2465 |
-4.59 |
4.19 |
0.29 |
14.43 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
16 |
YHR042W |
NCP1 |
2511 |
0.27 |
0.72 |
0.17 |
4.27 |
2.00E-05 |
1.21E-01 |
1.22E-03 |
2.01E-03 |
|
17 |
YHR175W |
CTR2 |
2644 |
-1.38 |
1.08 |
0.13 |
8.32 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
18 |
YJL153C |
INO1, APR1 |
3057 |
-2.03 |
0.74 |
0.15 |
5.06 |
4.33E-07 |
2.63E-03 |
2.64E-05 |
6.25E-05 |
|
19 |
YKL220C |
FRE2 |
3507 |
-3.98 |
2.78 |
0.26 |
10.75 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
20 |
YLL051C |
FRE6 |
3668 |
-1.44 |
0.97 |
0.13 |
7.55 |
4.97E-14 |
3.02E-10 |
3.03E-12 |
1.78E-11 |
|
21 |
YLR034C |
SMF3 |
3716 |
0.04 |
0.72 |
0.16 |
4.41 |
1.04E-05 |
6.32E-02 |
6.35E-04 |
1.11E-03 |
|
22 |
YLR046C |
3728 |
-1.88 |
0.72 |
0.14 |
5.19 |
2.21E-07 |
1.34E-03 |
1.35E-05 |
3.44E-05 |
|
|
23 |
YLR056W |
ERG3, SYR1 |
3738 |
0.92 |
0.80 |
0.18 |
4.47 |
8.04E-06 |
4.88E-02 |
4.90E-04 |
8.71E-04 |
|
24 |
YLR126C |
3808 |
-2.03 |
1.00 |
0.15 |
6.85 |
8.07E-12 |
4.90E-08 |
4.92E-10 |
2.23E-09 |
|
|
25 |
YLR136C |
TIS11, CTH2 |
3818 |
-1.31 |
0.91 |
0.13 |
7.02 |
2.41E-12 |
1.46E-08 |
1.47E-10 |
7.30E-10 |
|
26 |
YLR205C |
3885 |
-2.91 |
1.19 |
0.20 |
5.87 |
4.47E-09 |
2.71E-05 |
2.72E-07 |
8.47E-07 |
|
|
27 |
YLR214W |
FRE1 |
3894 |
-1.18 |
1.51 |
0.13 |
11.62 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
28 |
YMR006C |
PLB2 |
4286 |
-0.84 |
0.61 |
0.14 |
4.39 |
1.16E-05 |
7.06E-02 |
7.10E-04 |
1.22E-03 |
|
29 |
YMR011W |
HXT2 |
4291 |
0.02 |
0.81 |
0.16 |
4.96 |
7.28E-07 |
4.42E-03 |
4.44E-05 |
1.00E-04 |
|
30 |
YMR058W |
FET3 |
4340 |
0.42 |
1.91 |
0.17 |
11.10 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
31 |
YMR251W |
4540 |
-4.28 |
1.19 |
0.27 |
4.33 |
1.48E-05 |
9.00E-02 |
9.05E-04 |
1.53E-03 |
|
|
32 |
YNL237W |
YTP1 |
4856 |
-4.34 |
1.25 |
0.28 |
4.50 |
6.86E-06 |
4.16E-02 |
4.18E-04 |
7.95E-04 |
|
33 |
YNL259C |
ATX1 |
4878 |
-0.06 |
0.96 |
0.16 |
5.95 |
2.90E-09 |
1.76E-05 |
1.77E-07 |
5.86E-07 |
|
34 |
YNR056C |
BIO5 |
5003 |
-2.74 |
1.45 |
0.19 |
7.60 |
3.38E-14 |
2.05E-10 |
2.06E-12 |
1.28E-11 |
|
35 |
YNR060W |
FRE4 |
5007 |
-3.64 |
1.22 |
0.24 |
5.03 |
4.96E-07 |
3.01E-03 |
3.02E-05 |
7.00E-05 |
|
36 |
YOL158C |
5181 |
-2.76 |
2.93 |
0.19 |
15.28 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
37 |
YOR334W |
MRS2 |
5524 |
-0.15 |
0.68 |
0.16 |
4.27 |
1.95E-05 |
1.18E-01 |
1.19E-03 |
1.97E-03 |
|
38 |
YOR381W |
FRE3 |
5571 |
-2.23 |
1.77 |
0.16 |
11.37 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
39 |
YOR382W |
5572 |
-2.86 |
2.86 |
0.20 |
14.42 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
40 |
YOR383C |
5573 |
-4.03 |
4.72 |
0.26 |
18.07 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
|
41 |
YOR384W |
FRE5 |
5574 |
-3.82 |
1.56 |
0.25 |
6.23 |
5.11E-10 |
3.10E-06 |
3.12E-08 |
1.29E-07 |
|
Down-regulated genes |
|||||||||||
|
1 |
YBR054W |
YRO2 |
273 |
1.28 |
-0.95 |
0.19 |
-5.12 |
3.11E-07 |
1.89E-03 |
1.90E-05 |
4.72E-05 |
|
2 |
YBR147W |
366 |
-1.68 |
-0.64 |
0.13 |
-4.87 |
1.13E-06 |
6.86E-03 |
6.90E-05 |
1.40E-04 |
|
|
3 |
YCL030C |
HIS4 |
547 |
1.80 |
-0.87 |
0.19 |
-4.50 |
6.95E-06 |
4.22E-02 |
4.24E-04 |
7.95E-04 |
|
4 |
YDL171C |
GLT1 |
857 |
-0.59 |
-0.87 |
0.15 |
-5.95 |
2.81E-09 |
1.70E-05 |
1.71E-07 |
5.86E-07 |
|
5 |
YEL039C |
CYC7 |
1502 |
-1.34 |
-0.69 |
0.13 |
-5.31 |
1.14E-07 |
6.91E-04 |
6.95E-06 |
1.92E-05 |
|
6 |
YER174C |
GRX4 |
1721 |
1.09 |
-0.92 |
0.18 |
-5.06 |
4.31E-07 |
2.61E-03 |
2.63E-05 |
6.25E-05 |
|
7 |
YFL014W |
HSP12, GLP1, HOR5 |
1751 |
1.18 |
-0.91 |
0.18 |
-4.95 |
7.57E-07 |
4.60E-03 |
4.62E-05 |
1.02E-04 |
|
8 |
YFR030W |
MET10 |
1836 |
0.54 |
-1.01 |
0.17 |
-5.79 |
7.61E-09 |
4.62E-05 |
4.64E-07 |
1.40E-06 |
|
9 |
YFR055W |
1862 |
-0.74 |
-0.69 |
0.14 |
-4.90 |
1.00E-06 |
6.07E-03 |
6.11E-05 |
1.27E-04 |
|
|
10 |
YGL009C |
1873 |
4.10 |
-1.27 |
0.23 |
-5.58 |
2.54E-08 |
1.54E-04 |
1.55E-06 |
4.40E-06 |
|
|
11 |
YGL117W |
1979 |
1.05 |
-1.25 |
0.18 |
-6.85 |
8.05E-12 |
4.89E-08 |
4.91E-10 |
2.23E-09 |
|
|
12 |
YGR088W |
CTT1 |
2212 |
-1.93 |
-0.63 |
0.14 |
-4.48 |
7.50E-06 |
4.55E-02 |
4.57E-04 |
8.34E-04 |
|
13 |
YGR286C |
BIO2 |
2409 |
0.97 |
-1.10 |
0.18 |
-6.11 |
1.09E-09 |
6.61E-06 |
6.65E-08 |
2.54E-07 |
|
14 |
YHL021C |
2440 |
-0.19 |
-0.97 |
0.16 |
-6.17 |
7.25E-10 |
4.40E-06 |
4.42E-08 |
1.76E-07 |
|
|
15 |
YJR137C |
ECM17, MET5 |
3263 |
0.42 |
-0.85 |
0.17 |
-4.92 |
8.71E-07 |
5.28E-03 |
5.31E-05 |
1.12E-04 |
|
16 |
YKL148C |
SDH1 |
3436 |
-1.12 |
-0.77 |
0.13 |
-5.91 |
3.56E-09 |
2.16E-05 |
2.17E-07 |
6.97E-07 |
|
17 |
YLL041C |
SDH2 |
3658 |
-0.49 |
-0.90 |
0.15 |
-6.05 |
1.50E-09 |
9.10E-06 |
9.15E-08 |
3.25E-07 |
|
18 |
YLR304C |
ACO1, GLU1 |
3985 |
2.05 |
-0.88 |
0.20 |
-4.48 |
7.56E-06 |
4.59E-02 |
4.61E-04 |
8.34E-04 |
|
19 |
YMR021C |
MAC1, CUA1 |
4301 |
-0.43 |
-1.83 |
0.15 |
-12.17 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
0.00E+00 |
|
20 |
YOR356W |
5546 |
-0.03 |
-0.80 |
0.16 |
-4.93 |
8.45E-07 |
5.13E-03 |
5.16E-05 |
1.12E-04 |
|
|
|
|||||||||||
|
Candidates for differentially-expressed genes in the mac1 cDNA microarray experiment defined as those outside the adjusted supsmu-based 99.998%-STIs (unadjusted p-value ≤ 0.00002). The study monitored transcripts in a mac1 knockout and wild-type S. cerevisiae. RN, row number; ORF name, systematic name for open reading frame; Synonyms, alternative gene names (if any); CIN, case index numbers used in scatter plots to identify data points; log2(Cy3), predictor variable (log base 2 transformed Cy3 intensity value); log2(Cy5/Cy3), log base 2 of Cy5/Cy3 ratio (here ratios are residuals); RSE, residual scale estimator (for data points represented in the table it is based on supsmu non-parametric regression smoother); SR, standardized residuals (log2(Cy5/Cy3) divided by RSE); p, unadjusted p-values based on statistics for two-sided tolerance intervals; p', Bonferroni adjusted p-values using N = 6,068; p'', Bonferroni adjusted p-values using k = 61, q, q-values calculated using qvalue() function [45,46] (see Figure 24 supporting q-value calibration). p- and q-values are given in scientific notation and 0.00E+00 means that a value was less than 10-16. |
|||||||||||
|
Loguinov et al. Genome Biology 2004 5:R18 doi:10.1186/gb-2004-5-3-r18 |
|||||||||||
