Table 6.

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

	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

^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].