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