Table 2.
Significantly enriched COG functional categories in cross-condition and cross-strain comparisons
| Non-directional(a) | Directional(b) | |||
|---|---|---|---|---|
| COG functional category | OR(c) | FDR(d) | OR(e) | FDR(d) |
| MC58 cross-condition comparisons | ||||
| Saliva ↔ Blood | ||||
| Nucleotide transport and metabolism (COG F) | 2.66 | 0.044 | n.s. | n.s. |
| Energy metabolism and conversion (COG C) | n.s. | n.s. | 0.18 | 0.024 |
| Cell wall/membrane/envelope biogenesis (COG M) | n.s. | n.s. | 0.31 | 0.020 |
| Posttranslational modification, protein turnover, chaperones (COG O) | n.s. | n.s. | 0.13 | 0.023 |
| Not in COG | n.s. | n.s. | 6.53 | <0.001 |
| Blood ↔ CSF | ||||
| Not in COG | n.s. | n.s. | 0.06 | <0.001 |
| MC58 versus α522 cross-strain comparisons | ||||
| Blood | ||||
| Energy metabolism and conversion (COG C) | 2.25 | 0.008 | 11.6 | <0.001 |
| Cell wall/membrane/envelope biogenesis (COG M) | n.s. | n.s. | 0.19 | <0.001 |
| Saliva ↔ Blood | ||||
| Energy metabolism and conversion (COG C) | 2.99 | <0.001 | >5.33 | <0.001 |
| Translation, ribosomal structure and biogenesis (COG J) | n.s. | n.s. | 0.04 | <0.001 |
| Cell wall/membrane/envelope biogenesis (COG M) | n.s. | n.s. | 0.09 | 0.003 |
| Blood ↔ CSF | ||||
| Energy metabolism and conversion (COG C) | 3.27 | <0.001 | n.s. | n.s. |
(a) Comparison of differently versus non-differently expressed genes to identify COG categories that are affected by differential expression in general
(b) Comparison of differentially expressed genes to identify COG categories that are significantly affected by regulation in a distinct direction (gene expression asymmetry)
(c) Odds ratios based on Fisher’s exact test. Values greater than 1 indicate that significantly differentially expressed genes are enriched for genes from the corresponding COG functional class
(d) False discovery rate based on p-values from Fisher’s exact test and the Benjamini-Hochberg multiple testing correction with a significance cut-off of FDR < 0.05
(e) For cross-condition comparisons, values greater than 1 indicate that genes highly expressed in blood were enriched for the respective COG category. In cross-strain comparisons, values greater than 1 indicate that the respective COG category is significantly highly expressed or upregulated in strain MC58