TABLE 2.
Location and function of gene products of significantly differentially regulated mRNAs in hfq+ wild-type versus hfq mutant microarray expression analysis
| Category | Total significant genes (n = 120)c |
Upregulated genes (n = 48)d |
Downregulated genes (n = 72)e |
||||||
|---|---|---|---|---|---|---|---|---|---|
| Observedf | Expectedg | P < 0.05h | Observedf | Expectedg | P < 0.05h | Observedf | Expectedg | P < 0.05h | |
| Locationa | |||||||||
| Cytoplasmic | 79 | 76 | 21 | 30 | 2.5 × 10−3 | 58 | 46 | 7.9 × 10−4 | |
| Integral membrane protein | 20 | 21 | 10 | 8 | 10 | 12 | |||
| Membrane anchored | 2 | 4 | 1 | 2 | 1 | 3 | |||
| Membrane lipoprotein | 1 | 0 | 1 | 0 | 0 | 0 | |||
| Outer membrane β-barrel protein | 8 | 1 | 9.2 × 10−5 | 6 | 1 | 2.2 × 10−5 | 2 | 1 | |
| Periplasmic | 10 | 10 | 9 | 4 | 1.0 × 10−2 | 1 | 6 | 1.3 × 10−2 | |
| Gene product typeb | |||||||||
| Carrier | 4 | 2 | 1 | 1 | 3 | 1 | |||
| Partial information | 2 | 4 | 2 | 2 | 0 | 2 | |||
| Enzyme | 40 | 29 | 6.1 × 10−3 | 12 | 12 | 28 | 17 | 2.2 × 10−3 | |
| Factor | 15 | 4 | 8.5 × 10−6 | 4 | 2 | 11 | 2 | 2.0 × 10−5 | |
| Phage/IS | 2 | 9 | 5.8 × 10−5 | 1 | 3 | 1 | 5 | 2.7 × 10−2 | |
| Unknown function | 1 | 13 | 2.4 × 10−5 | 1 | 5 | 2.8 × 10−2 | 0 | 8 | 3.5 × 10−4 |
| Regulator | 1 | 6 | 9.1 × 10−3 | 1 | 3 | 0 | 4 | 1.9 × 10−2 | |
| Transporter | 27 | 9 | 2.1 × 10−7 | 17 | 4 | 3.5 × 10−8 | 10 | 5 | 2.6 × 10−2 |
| Structural component | 14 | 2 | 9.6 × 10−8 | 0 | 1 | 14 | 1 | 1.1 × 10−10 | |
| Carrier, predicted | 1 | 1 | 0 | 0 | 1 | 1 | |||
| Regulator, predicted | 3 | 4 | 1 | 2 | 2 | 3 | |||
| Transporter, predicted | 7 | 7 | 5 | 3 | 2 | 4 | |||
Location of gene products as described in reference 38. Only categories containing the observed genes are displayed.
Type of gene product as described in reference 38. Only categories containing observed genes are displayed.
Genes with significantly differentially regulated mRNAs from hfq+ versus hfq mutant microarrays as identified by SAM and that also changed levels at least 1.5-fold (120 genes).
Upregulated genes have mRNAs that increased in hfq mutants (48 genes).
Downregulated genes have mRNAs that decreased in hfq mutants (72 genes).
Number of gene products in each category.
Expected number of gene products in each category based on the total number of gene products for the entire genome (38).
Probability of number of observed genes in category based on the expected number using binomial statistics. Only categories with P < 0.05 are listed and deemed significant.