TABLE 1.
Summary of changes in expression of genes examined by DNA microarray, real-time PCR, and Northern and dot blot hybridizations
| ORF, product | Change in expressiona for growth on:
|
|||||||
|---|---|---|---|---|---|---|---|---|
| Lactose vs glucose
|
Maltose vs glucose
|
|||||||
| Microarrayb | Real-time PCRc | Northern blot | Dot blot | Microarrayb | Real-time PCRc | Northern blot | Dot blot | |
| TM0031 | 0.30 | 0.60 ± 0.10 | ND | ND | 0.24 | 0.05 ± 0.02 | ND | ND |
| TM0115 | 7.10 | ND | ND | + | No change | ND | ND | ⊘ |
| TM0310 | 4.05 | 18.91 ± 2.42 | ND | + | No change | 0.87 ± 0.49 | ND | ⊘ |
| TM0379, Nox | 2.79 | 1.24 ± 0.06 | ND | ND | 2.49 | 1.7 ± 0.62 | ND | ND |
| TM0381, PdhD | 2.22 | 1.79 ± 0.83 | ND | ND | No change | 2.92 ± 1.79 | ND | ND |
| TM1190, GalK | 6.41 | 19.58 ± 11.13 | No change | + | No change | 0.56 ± 0.18 | No change | ⊘ |
| TM1191, GalT | 6.65 | ND | ⊘ | ND | No change | ND | ⊘ | ND |
| TM1192, GalA | 6.23 | ND | ⊘ | ND | No change | ND | ⊘ | ND |
| TM1193, LacZ1 | 5.45 | 11.13 ± 2.20 | ⊘ | + | No change | 1.11 ± 0.64 | ⊘ | ⊘ |
| TM1194 | 5.46 | ND | ⊘ | ND | No change | ND | ⊘ | ND |
| TM1195, LacZ2 | 7.95 | 25.01 ± 4.97 | ++ | + | No change | 0.91 ± 0.23 | ⊘ | ⊘ |
| TM1196 | 6.30 | ND | + | ND | No change | ND | ⊘ | ND |
| TM1197 | 7.16 | ND | + | + | No change | ND | ⊘ | ⊘ |
| TM1198 | 6.79 | ND | ⊘ | ND | No change | ND | ⊘ | ND |
| TM1199 | 8.26 | ND | ++ | ND | No change | ND | + | ND |
| TM1200 | 2.83 | ND | + | ND | No change | ND | No change | ND |
| TM1201 | 5.52 | ND | + | ND | No change | ND | ⊘ | ND |
| TM1202, MalG1 | 5.45 | ND | + | ND | No change | ND | ⊘ | ND |
| TM1203, MalF1 | 7.28 | ND | + | ND | No change | ND | No change | ND |
| TM1204, MalE1 | 5.82 | 26.54 ± 6.48 | +++ | +++ | No change | 1.16 ± 0.46 | No change | + |
| TM1216 | 3.55 | 3.36 ± 1.36 | ND | ND | 3.53 | 4.13 ± 2.20 | ND | ND |
| TM1837, MalF2 | <2 | ND | ND | ⊘ | No change | ND | ND | ⊘ |
| TM1839, MalE2 | 2.40 | 41.57 ± 9.41 | ND | ++ | 3.28 | 26.12 ± 9.43 | ND | ++ |
| TM1840, AmyA | <2 | ND | ND | ⊘ | No change | ND | ND | ⊘ |
Symbols and abbreviations used in the table: +, up-regulation; ⊘, signal below detection; ND, not determined (gene expression was not examined using that method). The degree of change was assessed arbitrarily; in the following definitions, x is the determined ratio for the respective method. No change, 2 > x > 0.5 (microarray) or 1 > x > 0.5 (real-time PCR); +, 4 > x ≥ 2 (microarray), 5 > x > 1 (real-time PCR), or above background and stronger than the signal in glucose or no signal in glucose (dot blot and Northern blot); ++, 6 > x ≥ 4 (microarray), 10 > x > 5 (real-time PCR), or good signal intensity (dot blot and Northern blot); +++, x ≥ 6 (microarray), x > 10 (real-time PCR), or signal intensity is oversaturated (dot blot and Northern blot).
The false-discovery rate was 1.5%.
The expression ratios (± standard deviations) were calculated as means of the starting quantities of transcripts obtained with cells grown on either lactose or maltose divided by the means of those obtained from glucose-grown cells (from three assays).