Table 2.
Gene Ontology comparison.
| 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) |
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.
* Number of genes in the Affymetrix list annotated to the GO biological process Immunity and defense.
§Adjusted P-value derived from the binomial statistics testing the significance of the enrichment of the Immunity and defense GO category in Affymetrix list.