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Table 6 Distributions of expression differences of genes in functional categories compared with the overall differences distribution

From: Infection and genotype remodel the entire soybean transcriptome

  Functional categoryb
Fold change Rangea Disease & Defense Signal Transduction Transcription Intracellular Traffic Cell Structure Metabolism
Full < 0.0001c < 0.0001 < 0.0001 0.0008 0.006 < 0.0001
± 2.0X 0.03 0.0002 < 0.0001 0.002 < 0.0001 < 0.0001
± 1.5X 0.34 0.018 < 0.0001 0.017 0.0003 < 0.0001
± 1.2X 0.57 0.37 0.0008 0.23 0.36 0.0004
  1. aThe fold changes were calculated by contrast analysis with SAS Proc Mixed using GC-RMA normalized data. "Full" = full range from the greatest down-regulation to the greatest up-regulation; "± 2.0X" = from down-regulated 2.0x to up-regulated 2.0x; "± 1.5X" = from 1.5x down-regulated to 1.5x up-regulated; "± 1.2X" = from -1.2x down-regulated to 1.2x up-regulated. bFunctional category of each gene drawn from annotation of the Affymetrix soybean GeneChip by the Goldberg group at the University of California, Los Angeles http://estdb.biology.ucla.edu/seed. cp-value obtained by resampling for the Kolmogorov-Smirnov test for distribution differences between a particular functional category and the whole gene set for genes with significant infection responses in the lower court of Sloan; p values were adjusted for FDR by the TST method. Results for other cultivars and infection courts are shown [see Additional file 8].