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Table 1 Linear mixed-model analysis (LMMA) of soybean gene expression changes under infection by P. sojae.

From: Infection and genotype remodel the entire soybean transcriptome

    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
  1. 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.