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Table 3 Comparison of the differentially regulated genes in this study and three earlier studies based on COG sub-categories

From: Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm

Functional group classification based on COG Beloin et al. [40] Domka et al. [42] Hancock et al. [43] This study
E. coli strain E. coli K-12 E. coli K-12 ABU E. coli Ocular E. coli
Regulation Up Down Up Down Up Down Up Down
Cellular processes and signaling
 M. Cell wall/membrane/envelope biogenesis 19 9 9 8 4 25 14 14
 D. Cell cycle control, mitosis and meiosis 2 1 0 0 3 6 14 14
 N. Cell motility NA NA 32 1 1 0 7 19
 O. Post-translational modification, protein turnover, and chaperones 13 13 13 7 25 56 8 11
 T. Signal transduction mechanisms 5 0 11 3 12 2 7 5
 U. Intracellular trafficking, secretion, and vesicular transport NA NA 28 1 2 17 8 19
 V. Defense mechanisms NA NA 4 0 1 0 1 0
 Sub-total 39 23 97 20 48 106 59 82
Information storage and processing
 A. Transcription, RNA processing and modification 11 5 17 7 44 8 12 6
 L. Replication, recombination and repair 10 7 5 1 17 14 16 10
 Sub-total 21 12 22 8 61 22 28 16
Metabolism
 C. Energy production and conversation 23 9 23 16 12 34 12 18
 E. Amino acid transport and metabolism 9 22 20 15 5 36 20 17
 F. Nucleotide transport and metabolism 0 3 8 1 6 8 5 5
 G. Carbohydrate transport and metabolism 16 22 27 5 13 23 26 12
 H. Coenzyme transport and metabolism 3 5 6 1 9 14 5 7
 I. Lipid transport and metabolism 7 0 5 3 3 8 2 5
 P. Inorganic ion transport and metabolism 12 6 24 9 14 7 4 8
 Q. Secondary metabolites biosynthesis, transport and catabolism 2 1 5 0 2 7 5 2
 Sub-total 72 68 118 50 64 137 79 74
Unknown and general prediction only 121 86 53 6 57 23 24 29
Total 253 189 290 84 230 288 190 201
  1. The figures in each column indicate the number of genes up or down regulated in each category. Comparison between the four studies in terms of genes up or down regulated are not anticipated to be identical but the trends may be similar. For instance the number of genes up or down regulated when ABU E. coli is compared with ocular E. coli is similar for category V, L, F and I. Such comparisons could also be done between ocular E. coli and the other two strains of E. coli