Table 5 Statistics of differentially expressed genes in Cluster of Orthologous Genes*
Comparison | WG-W3110 | WGM-WG | WGMC-WGM | WHIC-WGMC | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
COG | U | D | T | U | D | T | U | D | T | U | D | T | |
A | RNA processing and modification | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
B | Chromatin structure and dynamics | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
C | Energy production and conversion | 29 | 4 | 33 | 8 | 28 | 36 | 0 | 0 | 0 | 24 | 35 | 59 |
D | Cell cycle control, cell division, chromosome partitioning | 0 | 1 | 1 | 2 | 0 | 2 | 0 | 0 | 0 | 2 | 2 | 4 |
E | Amino acid transport and metabolism | 11 | 11 | 22 | 12 | 20 | 32 | 0 | 0 | 0 | 15 | 23 | 38 |
F | Nucleotide transport and metabolism | 6 | 5 | 11 | 3 | 4 | 7 | 0 | 0 | 0 | 4 | 10 | 14 |
G | Carbohydrate transport and metabolism | 62 | 4 | 66 | 16 | 28 | 44 | 0 | 2 | 2 | 24 | 22 | 46 |
H | Coenzyme transport and metabolism | 0 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 3 | 7 |
I | Lipid transport and metabolism | 10 | 1 | 11 | 1 | 9 | 10 | 0 | 0 | 0 | 11 | 2 | 13 |
J | Translation, ribosomal structure and biogenesis | 2 | 4 | 6 | 3 | 0 | 3 | 0 | 0 | 0 | 1 | 0 | 1 |
K | Transcription | 17 | 8 | 25 | 13 | 14 | 27 | 1 | 1 | 2 | 15 | 25 | 40 |
L | Replication, recombination and repair | 1 | 6 | 7 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 5 | 6 |
M | Cell wall/membrane/envelope biogenesis | 2 | 10 | 12 | 7 | 3 | 10 | 0 | 1 | 1 | 16 | 4 | 20 |
N | Cell motility | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
O | Post-translational modification, protein turnover, and chaperones | 0 | 3 | 3 | 3 | 1 | 4 | 0 | 0 | 0 | 9 | 6 | 15 |
P | Inorganic ion transport and metabolism | 10 | 4 | 14 | 6 | 6 | 12 | 0 | 0 | 0 | 11 | 19 | 30 |
Q | Secondary metabolites biosynthesis, transport, and catabolism | 4 | 0 | 4 | 1 | 1 | 2 | 0 | 0 | 0 | 2 | 0 | 2 |
R | General function prediction only | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
S | Function unknown | 29 | 19 | 48 | 32 | 14 | 46 | 0 | 4 | 4 | 59 | 35 | 94 |
T | Signal transduction mechanisms | 6 | 2 | 8 | 0 | 5 | 5 | 0 | 0 | 0 | 9 | 6 | 15 |
U | Intracellular trafficking, secretion, and vesicular transport | 1 | 0 | 1 | 3 | 0 | 3 | 0 | 1 | 1 | 3 | 2 | 5 |
V | Defense mechanisms | 0 | 1 | 1 | 2 | 0 | 2 | 0 | 0 | 0 | 3 | 1 | 4 |
W | Extracellular structures | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Y | Nuclear structure | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Z | Cytoskeleton | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
a | Multi-COG | 3 | 1 | 4 | 3 | 3 | 6 | 0 | 2 | 2 | 5 | 3 | 8 |
- | Without COG | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Comparison | WGM-W3110 | WGMC-W3110 | WHIC-W3110 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
COG | U | D | T | U | D | T | U | D | T | |
A | RNA processing and modification | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
B | Chromatin structure and dynamics | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
C | Energy production and conversion | 17 | 1 | 18 | 18 | 1 | 19 | 42 | 41 | 83 |
D | Cell cycle control, cell division, chromosome partitioning | 2 | 1 | 3 | 3 | 1 | 4 | 2 | 0 | 2 |
E | Amino acid transport and metabolism | 9 | 8 | 17 | 11 | 3 | 14 | 30 | 29 | 59 |
F | Nucleotide transport and metabolism | 4 | 1 | 5 | 5 | 1 | 6 | 8 | 11 | 19 |
G | Carbohydrate transport and metabolism | 38 | 1 | 39 | 34 | 3 | 37 | 62 | 20 | 82 |
H | Coenzyme transport and metabolism | 1 | 1 | 2 | 0 | 2 | 2 | 3 | 12 | 15 |
I | Lipid transport and metabolism | 7 | 0 | 7 | 6 | 0 | 6 | 15 | 4 | 19 |
J | Translation, ribosomal structure and biogenesis | 2 | 0 | 2 | 2 | 0 | 2 | 4 | 5 | 9 |
K | Transcription | 10 | 2 | 12 | 12 | 1 | 13 | 34 | 25 | 59 |
L | Replication, recombination and repair | 0 | 1 | 1 | 0 | 3 | 3 | 5 | 15 | 20 |
M | Cell wall/membrane/envelope biogenesis | 8 | 5 | 13 | 6 | 11 | 17 | 18 | 13 | 31 |
N | Cell motility | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
O | Post-translational modification, protein turnover, and chaperones | 6 | 2 | 8 | 7 | 1 | 8 | 25 | 11 | 36 |
P | Inorganic ion transport and metabolism | 10 | 1 | 11 | 9 | 0 | 9 | 25 | 36 | 61 |
Q | Secondary metabolites biosynthesis, transport, and catabolism | 1 | 0 | 1 | 2 | 0 | 2 | 6 | 0 | 6 |
R | General function prediction only | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
S | Function unknown | 44 | 5 | 49 | 62 | 11 | 73 | 151 | 73 | 224 |
T | Signal transduction mechanisms | 3 | 0 | 3 | 2 | 0 | 2 | 13 | 7 | 20 |
U | Intracellular trafficking, secretion, and vesicular transport | 2 | 0 | 2 | 0 | 0 | 0 | 4 | 4 | 8 |
V | Defense mechanisms | 1 | 0 | 1 | 1 | 0 | 1 | 3 | 5 | 8 |
W | Extracellular structures | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Y | Nuclear structure | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Z | Cytoskeleton | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
a | Multi-COG | 3 | 2 | 5 | 0 | 2 | 2 | 6 | 4 | 10 |
- | Without COG | 2 | 0 | 2 | 2 | 0 | 2 | 3 | 5 | 8 |