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Table 3 Strain-specific differential expression in Toxoplasma gondii.

From: A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

  Number of genes Significant up- or down-regulation in:   
  Total Expressed in tachyzoites2 Any strain ( significance3) RH (type I) Pru (type II) VEG (type III) Other pattern
All genes in genome 7,793 3,986 2,078 477 570 193 838
GO-annotated genes 1(process annotations only) 2,074 1,360 677 143 218 60 256
Gene-GO Slim mappings 1 2,764 1,805 885 193 272 80 340
DNA metabolism 140 62 <2e-7 31 <0.01 8 7 0.03 4 12
RNA metabolism 250 177 0 .02 660 .03 16 19 4 27
Protein metabolism 806 574 <10e-6 288 <0.01 61 105 <0.01 21 101
Other metabolic process 528 331 179 31 58 14 76 0 .04
Other biological process 90 56 32 10 0.05 12 0 0.05 10
Transport 456 297 153 38 36 17 62
Signal transduction 85 54 29 7 8 3 11
Cell cycle/proliferation 52 28 0.05 13 2 5 4 0.02 2 0.04
Cell organization/biogenesis 238 151 70 16 14 0.02 10 30
Cell adhesion 17 8 2 0.05 1 0 1 0
Stress response 102 65 22 0.01 3 8 2 9
Unannotated genes 5,719 2,626 1,401 333 352 133 582
  1. 1 Multiple GO annotations are available for some genes, and some GO annotations map to multiple GO slim categories (although multiple annotations may also map to the same category). 2,074 genes include 2,979 GO annotations, corresponding to 3,503 GO Slims, for a total of 2,764 gene-GO Slim mappings.
  2. 2 Assessed using a 10% false discovery rate (see text for details).
  3. 3 Differential expression determined as described in the text. P-values represent enrichment for GO Slim terms, as determined by the hypergeometric distribution (only values less than 0.05 are shown). Green shading implies under-representation, while yellow shading implies over-representation.