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Table 2 Significantly enriched COG functional categories in cross-condition and cross-strain comparisons

From: Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

  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.
  1. (a) Comparison of differently versus non-differently expressed genes to identify COG categories that are affected by differential expression in general
  2. (b) Comparison of differentially expressed genes to identify COG categories that are significantly affected by regulation in a distinct direction (gene expression asymmetry)
  3. (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
  4. (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
  5. (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