TABLE 2.

Location and function of gene products of significantly differentially regulated mRNAs in hfq+ wild-type versus hfq mutant microarray expression analysis

CategoryTotal significant genes (n = 120)cUpregulated genes (n = 48)dDownregulated genes (n = 72)e
ObservedfExpectedgP < 0.05hObservedfExpectedgP < 0.05hObservedfExpectedgP < 0.05h
Locationa
    Cytoplasmic797621302.5 × 10−358467.9 × 10−4
    Integral membrane protein20211081012
    Membrane anchored241213
    Membrane lipoprotein101000
    Outer membrane β-barrel protein819.2 × 10−5612.2 × 10−521
    Periplasmic1010941.0 × 10−2161.3 × 10−2
Gene product typeb
    Carrier421131
    Partial information242202
    Enzyme40296.1 × 10−3121228172.2 × 10−3
    Factor1548.5 × 10−6421122.0 × 10−5
    Phage/IS295.8 × 10−513152.7 × 10−2
    Unknown function1132.4 × 10−5152.8 × 10−2083.5 × 10−4
    Regulator169.1 × 10−313041.9 × 10−2
    Transporter2792.1 × 10−71743.5 × 10−81052.6 × 10−2
    Structural component1429.6 × 10−8011411.1 × 10−10
    Carrier, predicted110011
    Regulator, predicted341223
    Transporter, predicted775324
  • a Location of gene products as described in reference 38. Only categories containing the observed genes are displayed.

  • b Type of gene product as described in reference 38. Only categories containing observed genes are displayed.

  • c 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).

  • d Upregulated genes have mRNAs that increased in hfq mutants (48 genes).

  • e Downregulated genes have mRNAs that decreased in hfq mutants (72 genes).

  • f Number of gene products in each category.

  • g Expected number of gene products in each category based on the total number of gene products for the entire genome (38).

  • h 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.