Table 4.
Enrichment of regulons for genes within COG functional categories
|
DNA motif ID |
TF |
COG functional category |
−log10 (P-value) |
|---|---|---|---|
| Known TF-DNA motif pairs | |||
| c1373_e | crp | Carbohydrate transport and metabolism; energy production and conversion | 10.03, 3.38 |
| c2225_o | fadR | Lipid metabolism | 5.03 |
| c594_e | fnr | Energy production and conversion | 6.06 |
| c577_e | fruR | Carbohydrate transport and metabolism | 8.06 |
| c583_e | lexA | DNA replication, recombination and repair; cell division and chromosome partitioning | 10.54, 4.53 |
| c590_e | metJ | Amino acid transport and metabolism | 5.06 |
| c591_e | mlc | Energy production and conversion; carbohydrate transport and metabolism | 3.42, 3.19 |
| c582_e | purR | Nucleotide transport and metabolism | 9.28 |
| c595_e | trpR | Amino acid transport and metabolism | 4.27 |
| Novel TF-DNA motif pairs | |||
| c4574 | ascG | Carbohydrate transport and metabolism | 5.44 |
| c352_o | baeR | Cell envelope biogenesis, outer membrane | 3.33 |
| c580_e | cadC | Energy production and conversion; nucleotide transport and metabolism | 3.60, 2.65 |
| c489_o | hydG | Transcription | 3.33 |
| c6105_o | idnR | Energy production and conversion | 5.14 |
| c7434_o | lrhA | Amino acid transport and metabolism | 3.12 |
| c645_o | nlp | Nucleotide transport and metabolism; translation, ribosomal structure and biogenesis | 4.82, 5.14 |
| c646_o | ntrC | Amino acid transport and metabolism | 3.11 |
| c648_o | pdhR | Energy production and conversion | 5.55 |
| c647_o | xylR | Carbohydrate transport and metabolism | 4.47 |
| c417_e | yagA | Carbohydrate transport and metabolism | 3.25 |
| c419_o | ycfQ | Signal transduction mechanisms | 2.74 |
| c428_o | ydcN | Energy production and conversion | 4.35 |
| c428_e | ydfH | Energy production and conversion | 2.73 |
| c6271_e | ydhB | Energy production and conversion; cell envelope biogenesis, outer membrane | 2.91, 3.19 |
| c571_e | yfeR | Lipid metabolism; cell envelope biogenesis, outer membrane | 3.51, 3.00 |
| c581_e | yfeT | Nucleotide transport and metabolism | 2.77 |
| c477_o | yfhH | Energy production and conversion | 2.79 |
| c3037_o | yhjC | Translation, ribosomal structure and biogenesis | 9.94 |
| c498_o | yidZ | Translation, ribosomal structure and biogenesis | 2.65 |
| c474_o | yjfQ | Translation, ribosomal structure and biogenesis | 3.39 |
| c467_o | ynfL | Coenzyme metabolism | 3.32 |
| c641_o
|
yqhC
|
DNA replication, recombination and repair
|
3.06
|
-
P-values were calculated as the tail probability of the hypergeometric distribution for finding at least k genes from a particular COG functional category in a regulon of size n. Since we considered 21 functional categories, 2.4 × 10−3 was chosen as the P-value cutoff to give an overall significance level of 0.05 for each regulon. Associations of TFs and DNA motifs are made according to the MWM method.
