Table 1.
Linear mixed-model analysis (LMMA) of soybean gene expression changes under infection by P. sojae.
| Fixed factorsa | ||||||
| FDRb | Significant genesc | Genotyped | Treatmente | Timef | Genotype × Treatment | |
| 0.05 | BH | Number | 26,262 | 27,285 | 5,335 | 25,100 |
| Percent | 92.6 | 96.2 | 18.8 | 88.5 | ||
| TST | Number | 27,156 | 27,732 | 9,960 | 26,500 | |
| Percent | 95.8 | 97.8 | 35.1 | 93.5 | ||
| q-value | Number | 27,430 | 27,872 | 12,602 | 27,008 | |
| Percent | 96.8 | 98.3 | 44.4 | 95.3 | ||
| 0.01 | BH | Number | 25,062 | 26,761 | 2,965 | 23,552 |
| Percent | 88.4 | 94.4 | 10.5 | 83.1 | ||
| TST | Number | 25,923 | 27,139 | 4,453 | 24,669 | |
| Percent | 91.4 | 95.7 | 15.7 | 87.0 | ||
| q-value | Number | 26,337 | 27,316 | 5,561 | 25,206 | |
| Percent | 92.9 | 96.3 | 19.6 | 88.9 | ||
| 0.001 | BH | Number | 23,542 | 26,015 | 1,575 | 21,445 |
| Percent | 83.0 | 91.8 | 5.6 | 75.6 | ||
| TST | Number | 24,191 | 26,351 | 2,025 | 22,381 | |
| Percent | 85.3 | 92.9 | 7.1 | 78.9 | ||
| q-value | Number | 24,657 | 26,582 | 2,488 | 23,012 | |
| Percent | 87.0 | 93.8 | 8.8 | 81.2 | ||
| 0.0001 | BH | Number | 21,988 | 25,272 | 960 | 19,577 |
| Percent | 77.6 | 89.1 | 3.4 | 69.1 | ||
| TST | Number | 22,611 | 25,560 | 1,173 | 20,293 | |
| Percent | 79.8 | 90.2 | 4.1 | 71.6 | ||
| q-value | Number | 23,150 | 25,836 | 1,381 | 20,922 | |
| Percent | 81.7 | 91.1 | 4.9 | 73.8 | ||
aModel: y = Genotype + Treatment + Time + Genotype × Treatment + Block + Block × Genotype + Block × Treatment + Block × Time + Block × Genotype × Treatment + Error, where y refers to the log2 scale median polish summarized gene expression values, the main factors (Genotype, Treatment and Time) and the interaction Genotype × Treatment were fixed factors while all the remaining terms were random factors. GC-RMA background correction and quantile normalization were performed prior to median polish summarization. LMMA was carried out using Proc Mixed of SAS v9. bThe p-values for each of the fixed factors were computed based on normality assumption and adjusted for multiple testing using BH, TST and q-value methods at levels from 0.0001 to 0.05. cNumbers of detectable genes significant for each factor at the indicated adjusted p value, and percentages of the total number of detectable genes. dGenotypes were V71-370, Sloan and VPRIL9. eTreatments include Upper, Lower, and Mock. fTime refers to sample harvest time window at 9:00 am, 10:30 am, and 12:00 pm.