TABLE 3.
Quantitative comparison of changes in mRNA accumulation determined by HDOA analysis and Northern blotting
| ORF | Gene | CKI score | Avg fold change in mRNA accumulation ± SD
|
Ho: at 99% μ(A) = μ(N)c | ML34/ML51, Northern blottingd | |
|---|---|---|---|---|---|---|
| HDOAa | Northern blottingb | |||||
| YCL011C | GBP2 | 0.44 | 1.4 ± 0.2 | 2.5 ± 0.2 | Reject | 2.3 |
| YDL170W | UGA3 | 0.44 | 1.7 ± 0.5 | 1.6 ± 0.4 | Accept | 3.7 |
| YFL050C | ALR2 | 0.59 | 3.8 ± 3.0 | 4.2 ± 0.3 | Accept | 6.2 |
| YIL087C | 0.44 | 1.4 ± 0.2 | 1.8 ± 0.5 | Accept | 1.2 | |
| YKL001C | MET14 | 0.44 | 1.5 ± 0.3 | 1.6 ± 0.2 | Accept | 0.9 |
| YLR130C | 0.44 | 1.4 ± 0.4 | 1.8 ± 0.1 | Reject | 1.9 | |
| YOL001W | PHO80 | 0.47 | 2.1 ± 1.3 | 2.5 ± 0.4 | Accept | 2.7 |
| YCR020C | PET18 | 1.0 | 4.2 ± 0.8 | 7.1 ± 1.0 | Reject | 6.3 |
| YDR210W | 1.0 | 2.2 ± 0.3 | 5.1 ± 1.9 | Reject | 2.2 | |
| YEL073C | 1.0 | 11.0 ± 4.4 | 13.7 ± 5.5 | Accept | 6.3 | |
| YIL165C | 0.88 | 2.6 ± 0.6 | 2.7 ± 0.5 | Accept | 4.6 | |
| YLR014C | PPR1 | 0.19 | 2.0 ± 0.8 | 2.9 ± 0.5 | Accept | 3.4 |
| YLR363C | NMD4 | 0.84 | 3.4 ± 1.1 | 3.2 ± 0.5 | Accept | 3.4 |
| YML123C | PHO84 | −1.0 | −4.4 ± 1.4 | −3.3 ± 0.3 | Reject | |
| YNL046W | 1.0 | 2.8 ± 1.3 | 2.4 ± 0.4 | Accept | 2.8 | |
| YOL108C | INO4 | 0.9 | 2.2 ± 0.7 | 3.4 ± 1.9 | Accept | 2.3 |
| YOR303W | CPA1 | 0.81 | 1.8 ± 0.5 | 2.6 ± 0.2 | Reject | 2.2 |
Calculated from HDOA data, using four trials from each of four upf− derivatives of strain YRSy307 (upf1−, upf2−, upf3−, and upf123−) (n = 16 trials in all) compared with data from four trials for the UPF+ derivative of LRSy307.
mRNA accumulation was measured by quantitative Northern blot analysis. Values were calculated by comparing data from the upf123− and the UPF+ derivative of strain LRSy307. mRNAs for YCL011C, YDL170W, YFL050C, YIL165C, YKL001C, YLR130C, YLR363C, YNL046W, and YOR303W were tested at n = 4; all others were tested at n = 8.
Statistical similarities of the means associated with data from HDOA analysis and Northern blotting were compared by using two-tailed t test assuming unequal variances at α = 0.01. The null hypothesis (Ho) states that the means are equal [μ(A) = μ(N)], while the alternative hypothesis states that the means are not equal. Accepting the null hypothesis indicates that the mean calculations for both HDOA and Northern blot analyses are not statistically indistinguishable. Rejecting the null hypothesis indicates that the means are statistically different. μ(A), mean average fold change as measured by arrays: μ(N), mean average fold change as measured by Northern blotting.
mRNA accumulation was assayed by Northern blot analysis in strains ML34 (UPF1) and ML51 (upf1−) (see Materials and Methods; to test whether changes observed in strain LYRy307 were strain specific.