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Table 2 Gene Ontology comparison.

From: Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

GO classes Reference lists Affymetrix lists Illumina lists RNG-86 lists
  Affy 18373 Illum 16592 RNG 17550 Best 3800 (n = 3735) P < 0.001 (n = 1876) Best 3800 (n = 3756) Pc < 0.001 (n = 1990) Best 3800 (n = 3549) Pc < 0.001 (n = 5198)
Immunity and defense 1154 1124 1123 318 * (P < 10-5) § 189 (P < 10-8) 351 (P < 10-7) 205 (P < 10-7) 326 (P < 10-8) 383 (P < 0.09)
Intracellular signaling cascade 818 779 802 217 (P < 0.05) 118 (P < 0.05) 214 (ns) 118 (ns) 208 (P < 0.05) 272 (ns)
Lipid, fatty acid and steroid metabolism 673 647 655 189 (P < 10-3) 107 (P < 10-3) 196 (P < 0.05) 119 (P < 10-3) 178 (P < 0.05) 223 (ns)
Apoptosis 470 457 458 130 (P < 0.05) 77 (P < 0.05) 127 (ns) 75 (ns) 132 (P < 0.05) 163 (ns)
Carbohydrate metabolism 520 502 496 132 (ns) 69 (ns) 147 (P < 0.05) 75 (ns) 143 (P < 10-3) 190 (P < 0.05)
Protein metabolism and modification 2426 2316 2340 584 (P < 10-3) 283 (ns) 624 (P < 10-4) 342 (P < 10-3) 600 (P < 10-8) 836 (P < 10-6)
Signal transduction 2973 2866 2979 617 (ns) 374 (P < 10-3) 591 (ns) 350 (ns) 565 (ns) 733 (P < 10-6)
  1. GO biological process categories over represented in the lists of differentially expressed genes generated on each platform and according to two different selection criteria (the "Best 3800" probes or a Pc < 0.001). The table is ordered by the adjusted P-value of the test of association between RNG-86 list and GO categories. For each platform, list of DEG was compared to the list of all genes represented on the array. Genes belonging to several GO classes are included several times, once for each GO class that is associated with this gene.
  2. * Number of genes in the Affymetrix list annotated to the GO biological process Immunity and defense.
  3. §Adjusted P-value derived from the binomial statistics testing the significance of the enrichment of the Immunity and defense GO category in Affymetrix list.