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Table 1 Gene ontology analyses of up-regulated genes

From: Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus

Non-redundant GO categories Level Differentially
expressed (%)
Total genes in
the class (%)
P
Over-represented     
   Response to mechanical stimulus 4 1.07 (5) 0.03 6.36×10-4
   Response to wounding 4 2.99 (14) 0.78 1.17×10-7
   Response to abscisic acid stimulus 5 5.59 (24) 1.72 1.76×10-4
   Response to bacterium 5 3.73 (16) 0.77 1.31×10-4
   Response to cold 5 5.83 (25) 1.34 1.34×10-6
   Response to ethylene stimulus 5 4.43 (19) 1.17 2.84×10-4
   Response to heat 5 4.90 (21) 0.78 1.17×10-7
   Response to metal ion 5 2.56 (11) 0.63 1.13×10-2
   Response to oxidative stress 5 4.20 (18) 1.60 1.77×10-2
   Hyperosmotic salinity response 6 1.81 (6) 0.27 2.79×10-2
   Protein folding 6 6.04 (20) 2.36 1.16×10-2
   Response to desiccation 6 1.51 (5) 0.1 5.98×10-3
   Toxin catabolic process 6 2.42 (8) 0.24 1.14×10-2
   Programmed cell death 7 3.61 (9) 0.76 1.33×10-2
   Response to absence of light 7 1.20 (3) 0.03 2.75×10-2
   Systemic Acquired Resistance 8 4.67 (7) 0.42 1.04×10-3
Under-represented     
   Organelle organization and biogenesis 4 1.07 (5) 5.19 3.42×10-4
   DNA metabolic process 5 0.70 (3) 3.56 1.62×10-2
  1. Non-redundant GO categories identified as enriched among up-regulated genes in infected plants versus mock-inoculated plants. The percentages of genes belonging to each category are reported for the differentially expressed genes and for the A. thaliana genes present in the microarray. The absolute number of genes is reported in parenthesis for the differentially expressed set. P: FDR-corrected P-value for the Fisher's exact test in a 2 × 2 contingency table.