TABLE 2.
Overrepresented functional and gene ontology (GO) categories in the differentially expressed genes
| Functional category | Focal point | Focal point: no. of significant genes | Overall: no. of significant genes | No. of genes on the arrays | P-value | q-Value |
|---|---|---|---|---|---|---|
| Cell structure, membrane | D/A-TP3 | 43 | 131 | 784 | <0.001 | 0.03 |
| Cluster 2 | 43 | <0.001 | 0.003 | |||
| Cell structure, ribosome | FS/A-TP2 | 27 | 38 | 69 | 0.004 | 0.08 |
| D/A-TP1 | 23 | <0.001 | <0.001 | |||
| Cluster 1 | 33 | <0.001 | <0.001 | |||
| Overall | NA | <0.001 | <0.001 | |||
| Information transfer, protein related | D/A-TP1 | 35 | 65 | 295 | <0.001 | <0.001 |
| Cluster 1 | 45 | <0.001 | <0.001 | |||
| Overall | NA | <0.001 | 0.02 | |||
| Location, cytoplasm | D/A-TP1 | 50 | 140 | 849 | 0.007 | 0.1 |
| Cluster 1 | 68 | 0.003 | 0.07 | |||
| Location, inner membrane | D/A-TP3 | 32 | 99 | 531 | 0.005 | 0.09 |
| Overall | NA | 0.006 | 0.1 | |||
| Location, periplasmic space | D/A-TP1 | 9 | 14 | 128 | 0.003 | 0.07 |
| Metabolism, carbon compound utilization | FS/A-TP1 | 7 | 50 | 363 | 0.003 | 0.07 |
| Metabolism, energy metabolism (carbon) | Cluster 3 | 13 | 39 | 229 | 0.003 | 0.07 |
| Transport | D/A-TP3 | 32 | 104 | 616 | 0.006 | 0.1 |
| Cluster 2 | 33 | 0.002 | 0.07 | |||
| GO category | Focal point | Focal point: no. of significant genes | Overall no. of significant genes | No. of genes on the arrays | P-value | q-Value |
| Acetyl-CoA biosynthesis from pyruvate | Overall | NA | 2 | 2 | 0.03 | 0.18 |
| Amino acid activation | FS/A | 2 | 4 | 31 | 0.008 | 0.12 |
| Amino sugar biosynthesis | Cluster3 | 2 | 2 | 15 | 0.02 | 0.15 |
| Anaerobic respiration | Cluster3 | 7 | 22 | 139 | 0.03 | 0.18 |
| ATP-synthesis-coupled proton transport | Overall | NA | 9 | 12 | <0.001 | <0.001 |
| Carbohydrate catabolism | FS/A-TP1 | 8 | 36 | 235 | <0.001 | <0.001 |
| FS/A-TP3 | 3 | 0.03 | 0.19 | |||
| SS/A-TP1 | 8 | 0.004 | 0.07 | |||
| DNA catabolism | SS/A-TP4 | 2 | 3 | 49 | 0.01 | 0.12 |
| Fermentation | Cluster3 | 3 | 4 | 33 | 0.01 | 0.12 |
| Flagella biogenesis | Cluster3 | 3 | 5 | 35 | 0.02 | 0.17 |
| Glycerol metabolism | FS/A-TP1 | 2 | 5 | 16 | 0.02 | 0.14 |
| FS/A-TP4 | 3 | 0.003 | 0.06 | |||
| FS/A | 2 | 0.01 | 0.15 | |||
| D/A-TP2 | 2 | 0.01 | 0.12 | |||
| D/A | 2 | 0.005 | 0.07 | |||
| FS/SS-TP1 | 2 | 0.002 | 0.04 | |||
| FS/SS | 2 | 0.001 | 0.04 | |||
| Leucine biosynthesis | SS/A-TP4 | 2 | 2 | 16 | 0.004 | 0.06 |
| Polysaccharide biosynthesis | D/A-TP4 | 2 | 2 | 8 | 0.01 | 0.12 |
| Cluster2 | 2 | 0.02 | 0.14 | |||
| Protein biosynthesis | Overall | NA | 44 | 78 | <0.001 | <0.001 |
| FS/A-TP2 | 30 | 0.002 | 0.04 | |||
| D/A-TP1 | 28 | <0.001 | <0.001 | |||
| Cluster1 | 37 | <0.001 | <0.001 | |||
| Protein modification | Cluster2 | 3 | 5 | 64 | 0.02 | 0.14 |
| Purine nucleotide biosynthesis | Overall | NA | 5 | 10 | 0.01 | 0.14 |
| Translational attenuation | Overall | NA | 5 | 6 | <0.001 | 0.02 |
| Tryptophan biosynthesis | FS/A-TP4 | 2 | 4 | 11 | 0.03 | 0.19 |
| SS/A-TP4 | 2 | 0.02 | 0.15 |
For each category identified as overexpressed, the number of significant genes in the focal comparison and in the overall data set, the number of genes on the arrays, the P-values of the one-tail Fisher's exact tests, and the q-values of the false discovery rate are indicated. For example, the first line of the table indicates that 784 genes represented on the array encode for proteins associated with the structure of the membrane, that 131 of these genes are identified as differentially expressed in at least 1 of the 20 statistical comparisons performed, and that 43 genes are identified as differentially expressed between the evolved and the ancestor at the time point 3, which is more than would be expected if the significant genes were randomly distributed in the different functional categories, with a P-value <0.001 and a q-value of 0.03. NA indicates that the overall number of genes identified as differentially expressed is greater than would be randomly expected (for example, the 38 genes differentially expressed in the functional category “Cell structure, ribosome” is more than would be randomly expected).