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Table 5 Consistency of selected gene expression differences among independent experiments, measured by qRT-PCR and/or microarray.

From: Infection and genotype remodel the entire soybean transcriptome

     Pilot experiment   72-replicate experiment (array)  
     5 day   5 day (average upper and lower versus mock)  
Geno-typea Gene IDb Annotationc Inoc/Mock qRT array Wholef Subg A Sub B Sub C Sub D Sub E Sub F
V71-370 Gma.441.1.S1_at Ubiquitin (AtRUB1) [HK] meand 1.17 1.08 1.07 1.08 1.04 1.05 1.21 1.09 -1.01
    s.e.e 0.9 0.08 0.03 0.09 0.05 0.08 0.08 0.04 0.09
  Gma.16125.1.S1_s_at Ribosomal protein S27-like [HK] mean 1.12 1.16 1.15‡ 1.17 1.19 1.14 1.16 1.19 1.08
    s.e. 0.15 0.14 0.06 0.10 0.12 0.14 0.16 0.12 0.11
  GmaAffx.90824.1.S1_s_at 26S proteasome subunit RPN2a [HK] mean -1.25 -1.16 -1.08 -1.00 -1.23 -1.08 -1.12 1.00 -1.02
    s.e. 0.18 0.15 0.04 0.10 0.08 0.09 0.08 0.06 0.08
  GmaAffx.90181.1.A1_at Actin mean 2.0 1.25 -1.03 1.07 -1.00 -1.11 1.07 -1.11 -1.05
    s.e. 0.8 0.5 0.07 0.17 0.17 0.20 0.17 0.16 0.16
  GmaAffx.60616.1.S1_at Hcr9-OR2A mean -1.7 -1.5 -1.35‡ -1.28 -1.31 -1.20 -1.20 -1.37 -1.8
    s.e. 0.49 0.22 0.04 0.10 0.11 0.12 0.09 0.10 0.09
  Gma.447.1.S1_at Defense associated acid phosphatase mean -2.8 -1.47 -1.9‡ -1.34 -1.34 -2.9 -1.5 -2.8 -1.9
    s.e. 0.40 0.27 0.05 0.18 0.23 0.06 0.16 0.06 0.11
  GmaAffx.64261.1.A1_at Quinone oxidoreductase mean 3.6 8.5*‡ 5.6‡ 5.3 5.4 5.3 7.4 4.4 7.2
    s.e. 0.7 2.7 0.6 1.8 1.3 1.1 1.9 0.9 1.7
  Gma.6640.1.S1_at At5g66390 (secretory peroxidase) mean 1.5 1.46‡ 1.07‡ 1.06 1.15 -1.10 1.10 1.11 1.11
    s.e. 0.43 0.10 0.05 0.12 0.11 0.10 0.11 0.09 0.13
  GmaAffx.18905.1.S1_at Cell death associated protein mean 2.5 2.4‡ 2.3‡ 2.0 1.9 2.7 2.8 2.4 2.4
    s.e. 0.41 0.7 0.21 0.42 0.42 0.6 0.46 0.46 0.37
  Gma.17993.1.S1_at P21 protein mean 60 70‡ 30‡ 29 34 26 40 36 24
    s.e. 13 19 3.7 11 9 7 7 10 9
  GmaAffx.75675.1.A1_at Phenylalanine ammonia-lyase mean 3.9 7.6*‡ 4.4‡ 4.4 4.4 4.7 4.0 4.6 4.9
    s.e. 0.41 0.9 0.29 0.9 0.7 0.7 0.46 0.7 0.7
  GmaAffx.2799.1.A1_at NtPRp27-like protein mean 12 20‡ 7.8‡ 5.9 7.8 8.0 7.8 9.6 8.3
    s.e. 0.6 5 0.6 1.4 1.4 1.1 0.9 1.2 1.3
  Gma.16733.2.S1_at WRKY4 transcription factor mean 4.9 6.8‡ 2.9‡ 3.9 3.5 2.6 3.1 2.9 2.6
    s.e. 0.6 1.7 0.37 1.0 1.2 0.8 0.9 1.1 0.7
  GmaAffx.29692.1.S1_at Chitinase (class II) mean 1.9 2.9‡ 2.0‡ 2.4 2.1 1.6 1.9 1.8 2.2
    s.e. 0.47 0.7 0.11 0.34 0.27 0.22 0.20 0.29 0.23
  Gma.16911.1.S1_at Cytochrome P450 family protein mean -1.23 1.6 1.24‡ 1.07 1.20 1.29 1.21 1.28 1.47
    s.e. 0.26 0.33 0.05 0.11 0.11 0.11 0.11 0.10 0.08
  GmaAffx.7209.1.A1_at UDP-glucose 6-dehydrogenase mean -1.02 1.36 -1.02 1.09 1.17 -1.05 -1.03 -1.24 -1.01
    s.e. 0.10 0.21 0.07 0.14 0.22 0.11 0.13 0.13 0.15
  GmaAffx.47171.1.A1_at Putative resistance protein mean -1.03 1.43‡ 1.6‡ 1.35 1.5 1.5 1.6 1.7 1.9
    s.e. 0.12 0.38 0.08 0.17 0.17 0.21 0.16 0.16 0.19
  Gma.3473.1.S1_at Protein, small heat shock mean -1.26 -1.20 -1.7‡ 1.7 -1.6 -3.4 -1.7 -2.1 -2.3
    s.e. 0.26 0.22 0.06 0.30 0.16 0.08 0.14 0.11 0.08
  GmaAffx.90984.1.A1_at Germin-like protein mean 14 5.7‡ 2.1‡ 2.0 2.2 1.9 1.9 2.0 2.4
    s.e. 2.5 2.2 0.16 0.35 0.44 0.31 0.33 0.47 0.39
  GmaAffx.32612.1.S1_at HI4'OMT mean 18 24‡ 14‡ 9.6a 8.9a 20b 12a 21b 22b
    s.e. 1.8 6.5 1.5 3.2 2.3 3.3 2.8 4.7 6
  GmaAffx.90059.1.S1_at HcrVf2 protein mean 7.4 3.7‡ 3.0‡ 3.2 2.7 2.9 3.2 2.9 3.2
    s.e. 2.0 0.8 0.22 0.5 0.37 0.26 0.41 0.42 0.8
  GmaAffx.79817.1.S1_at SGT1 mean 1.13 1.04 -1.01 1.07 -1.10 1.00 -1.04 -1.11 1.13
    s.e. 0.14 0.07 0.04 0.15 0.08 0.14 0.06 0.05 0.07
Sloan Gma.441.1.S1_at Ubiquitin (AtRUB1) [HK] meand -1.04 1.19 1.12‡ 1.07 1.20 1.07 1.23 1.10 1.08
    s.e.e 0.10 0.14 0.04 0.09 0.06 0.09 0.12 0.08 0.11
  Gma.16125.1.S1_s_at Ribosomal protein S27-like [HK] mean -1.18 1.03 -1.07 1.02 -1.04 -1.14 1.10 -1.17 -1.14
    s.e. 0.5 0.18 0.06 0.08 0.06 0.15 0.22 0.07 0.10
  GmaAffx.90824.1.S1_s_at 26S proteasome subunit RPN2a [HK] mean 1.5 1.01 -1.06‡ -1.15 -1.03 -1.01 -1.06 -1.03 -1.07
    s.e. 0.20 0.11 0.04 0.09 0.06 0.13 0.09 0.06 0.04
  GmaAffx.90181.1.A1_at Actin mean -1.36 1.49‡ -1.19‡ -1.29 -1.18 -1.28 -1.13 -1.33 1.10
    s.e. 0.26 0.40 0.06 0.10 0.22 0.16 0.12 0.13 0.22
  GmaAffx.60616.1.S1_at Hcr9-OR2A mean -1.7 -2.2‡ -1.9‡ -1.45 -1.8 -2.0 -1.9 -1.7 -2.3
    s.e. 0.41 0.12 0.05 0.12 0.09 0.14 0.09 0.12 0.08
  Gma.447.1.S1_at Defense associated acid phosphatase mean -1.43 -1.47 -1.8‡ -1.8 -1.6 -2.0 -1.8 -2.2 -1.48
    s.e. 0.14 0.21 0.06 0.15 0.12 0.17 0.13 0.09 0.17
  GmaAffx.64261.1.A1_at Quinone oxidoreductase mean 3.1 2.3‡ 2.6‡ 3.9 4.7 -1.24 2.7 3.0 3.0
    s.e. 0.6 0.40 0.39 1.5 1.5 0.23 0.8 1.1 1.1
  Gma.6640.1.S1_at At5g66390 (secretory peroxidase) mean 1.14 -1.08 -1.16‡ -1.38 -1.21 -1.20 1.30 -1.10 -1.33
    s.e. 0.49 0.22 0.06 0.15 0.10 0.15 0.16 0.17 0.13
  GmaAffx.18905.1.S1_at Cell death associated protein mean 3.4 1.5‡ 2.9†‡ 3.5 4.5 2.1 3.2 2.9 2.2
    s.e. 0.5 0.32 0.27 0.9 0.7 0.5 0.7 0.6 0.39
  Gma.17993.1.S1_at P21 protein mean 72 94‡ 43a‡ 41a 45a 44a 21b 100c 55a
    s.e. 27 27 7 18 20 16 9 24 17
  GmaAffx.75675.1.A1_at Phenylalanine ammonia-lyase mean 9.3 15‡ 6.3‡ 7.2 7.7 6.0 4.4 7.2 6.2
    s.e. 2.8 2.7 0.44 1.3 1.2 1.1 0.40 1.5 0.7
  GmaAffx.2799.1.A1_at NtPRp27-like protein mean 14 15‡ 8.3‡ 5.8 8.6 9.8 6.0 11 11
    s.e. 2.4 3.4 0.7 0.8 1.5 1.9 1.0 2.5 1.9
  Gma.16733.2.S1_at WRKY4 transcription factor mean 5.8 5.3‡ 3.5‡ 6.9 3.8 2.7 4.3 3.1 2.3
    s.e. 1.3 1.2 0.44 2.2 1.1 0.8 1.1 1.1 0.5
  GmaAffx.29692.1.S1_at Chitinase (class II) mean 2.5 2.7‡ 3.1‡ 3.2 2.7 2.7 2.9 3.5 4.2
    s.e. 0.35 0.6 0.21 0.6 0.34 0.6 0.27 0.7 0.5
  Gma.16911.1.S1_at Cytochrome P450 family protein mean 3.4 4.0‡ 3.1‡ 2.9 3.4 2.9 2.8 4.2 3.0
    s.e. 0.8 1.0 0.18 0.5 0.37 0.40 0.28 0.46 0.44
  GmaAffx.7209.1.A1_at UDP-glucose 6-dehydrogenase mean 1.8 2.2‡ 1.02 1.49 1.28 -1.7 -1.08 1.16 1.04
    s.e. 0.27 0.6 0.11 0.21 0.28 0.12 0.14 0.31 0.26
  GmaAffx.47171.1.A1_at Putative resistance protein mean -1.07 1.08 1.21‡ 1.23 1.18 1.11 1.16 1.35 1.30
    s.e. 0.16 0.34 0.07 0.18 0.15 0.16 0.14 0.18 0.17
  Gma.3473.1.S1_at Protein, small heat shock mean -1.41 -1.6 -2.2‡ 1.03 -3.6 -3.3 -1.9 -2.4 -1.9
    s.e. 0.16 0.09 0.05 0.37 0.05 0.08 0.08 0.11 0.15
  GmaAffx.90984.1.A1_at Germin-like protein mean 5.3 2.5‡ -1.06 1.10 1.18 -1.18 -1.06 -1.12 -1.23
    s.e. 1.7 0.5 0.07 0.20 0.21 0.12 0.10 0.10 0.14
  GmaAffx.32612.1.S1_at HI4'OMT mean 57 16‡ 25a‡ 18a 22a 24a 18a 43b 41b
    s.e. 16 4.2 2.8 6 5 7 4.9 12 8
  GmaAffx.90059.1.S1_at HcrVf2 protein mean 3.9 2.5‡ 2.7‡ 5.5 4.0 1.3 2.3 2.8 2.4
    s.e. 1.1 0.38 0.25 0.8 0.7 0.17 0.35 0.44 0.7
  GmaAffx.79817.1.S1_at SGT1 mean 1.21 -1.19 -1.04 1.08 -1.02 1.01 -1.02 -1.08 -1.18
    s.e. 0.28 0.05 0.05 0.18 0.06 0.20 0.07 0.05 0.04
  1. aGenotypes used for this comparison were cultivars V71-370 and Sloan; b22 genes selected for qRT assays. cThe functional annotation of the selected genes. [HK] indicates housekeeping genes used to normalize the qRT-PCR results dThe average expression difference between inoculated and mock samples, calculated as a fold-change. Negative values indicate downward change in response to infection. The presence of letter suffixes (a, b, c) after mean values indicates the presence of significant variation among the subgroup means, as determined by Least Significant Difference with a cutoff of an FDR-adjusted p value of 0.05. In those cases, means with the same suffix are not significantly different from one another. If no suffixes are present, there are no significant differences among any of the means. Symbol * indicates gene expression differences measured by microarray analysis in the pilot experiment that differ significantly from the measurements obtained by qRT-PCR analysis, determined using t tests with a cutoff of an FDR-adjusted p value of 0.05. Symbol † indicates gene expression differences measured by microarray analysis in the whole 72 replicate experiment that differ significantly from the measurements obtained by microarray analysis in the pilot experiment, determined using t tests with a cutoff of an FDR-adjusted p value of 0.05. Symbol ‡ indicates expression changes in the pilot microarray experiment and the whole 72 replicate experiment that are significant at a cutoff of a TST-FDR-adjusted p value of 0.01. eThe standard errors are calculated from log-transformed expression differences from 3 technical replicates in the case of the qRT-PCR results, from 4 biological replicates in the case of the pilot array data, from 72 biological replicates in the whole main experiment, and from 12 biological replicates in the main experiment sub-groups. fAll the 72-replicates as a whole experiment. gSub-groups of the whole experiment each comprising 12 consecutive replicates.