Table 1.
Count of genes that are differentially expressed when comparing growth substrates predicted by several methods
| Genes | |||||
|---|---|---|---|---|---|
| Comparison | edgeR | DESeq2 | PoissonSeq | Consensusb | |
| MeOH vs Acetate | 621 | 341 | 400 | 201 (126d) | |
| MeOH vs TMA | 2839 | 258 | 2348 | 211 (112d) | |
| TMA vs Acetate | 2762 | 757 | 1955 | 645 (335d) | |
| Methylotrophic vs | 511 | 179 | 301 | 100 | |
| Acetotrophic | |||||
| Operonsa | |||||
| Comparison | DOOR2 | Microbes Online | ProOpDB | Rockhopper | Consensusc |
| MeOH vs Acetate | 205 (144) | 183 (110) | 189 (129) | 207 (151) | 157 |
| MeOH vs TMA | 202 (148) | 198 (117) | 211 (143) | 212 (158) | 163 |
| TMA vs Acetate | 662 (450) | 701 (343) | 667 (406) | 655 (469) | 571 |
| Methylotrophic vs | 112 (75) | 97 (53) | 91 (56) | 112 (79) | 76 |
| Acetotrophic |
aIntersection of the sets of differentially expressed genes predicted by the three methods. bCount of differentially expressed genes that are associated with reactions in the metabolic model. cThe differential expression procedure applied to reads summed over putative operons of a specific dataset, where the number reported is total genes called as differentially expressed, while the number in parenthesis is the total number of operons called as differentially expressed. dIntersection of the sets of differentially expressed genes predicted to be in differentially expressed operons (because operon structures were not conserved across the methods)