From: Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei
Functional category and CDS | Gene Name | Product | Pvalue (Bonferroni) common variance model | Pvalue (FDR) varmixt model | Expression sigH(hy)*/ | ratio$ sigH(wt)* |
---|---|---|---|---|---|---|
microarray | qPCR | |||||
Competence | ||||||
LSA0492 | comFA | DNA uptake machinery § | 1.54E-02 | > threshold | 1.5 ± 0.4 | 286 ± 88 |
LSA0493 | comFC | DNA uptake machinery | 0 | 3.56E-03 | 2.2 ± 0.2 | |
LSA1069 | comEC | DNA uptake machinery | 9.52E-10 | 1.31E-02 | 1.9 ± 0.2 | |
LSA1071 | comEA | DNA uptake machinery | 0 | 7.23E-03 | 2.5 ± 0.3 | 261 ± 115 |
LSA1301 | comGF | DNA uptake machinery | 0 | 2.71E-04 | 3 ± 2 | |
LSA1302 | comGE | DNA uptake machinery | 0 | 1.44E-06 | 3.7 ± 0.5 | |
LSA1303 | comGD | DNA uptake machinery | 0 | 2.21E-04 | 2.8 ± 0.3 | |
LSA1304 | comGC | DNA uptake machinery | 0 | 5.62E-12 | 7 ± 2 | 421 ± 104 |
LSA1305 | comGB | DNA uptake machinery | 1.02E-10 | 3.57E-02 | 2.0 ± 0.3 | |
LSA1306 | comGA | DNA uptake machinery | 3.17E-09 | 7.25E-03 | 1.9 ± 0.2 | |
LSA1771 | comC | DNA uptake machinery | 0 | 4.10E-06 | 3.2 ± 0.2 | 608 ± 199 |
DNA metabolism: replication, repair, recombination, RM | ||||||
LSA0008 | ssb | Single-stranded DNA binding protein | > threshold | 3.88E-02 | 1.4 ± 0.1 | 1.2 ± 0.3 |
LSA0146 | Putative DNA methyltransferase (apparently stand-alone) | 1.55E-04 | > threshold | 1.6 ± 0.4 | ||
LSA1299 | Putative DNA methyltransferase (apparently stand-alone) | 2.48E-08 | > threshold | 1.9 ± 0.4 | ||
LSA1338 | exoA | Exodeoxyribonuclease III | 1.36E-07 | > threshold | 1.8 ± 0.3 | |
Purines, pyrimidines, nucleosides and nucleotides | ||||||
LSA0533 | iunh2 | Inosine-uridine preferring nucleoside hydrolase | 1.14E-05 | > threshold | 1.7 ± 0.4 | |
Energy metabolism | ||||||
LSA1298 | ack2 | Acetate kinase | 4.27E-09 | > threshold | 1.9 ± 0.4 | |
Translation | ||||||
LSA0009 | rpsR | Ribosomal protein | 1.67E-02 | > threshold | 1.5 ± 0.4 | |
Regulatory function | ||||||
LSA0421 | Putative transcriptional regulator, MerR family | 0 | 3.56E-03 | 2.5 ± 0.5 | ||
Hypothetical protein | ||||||
LSA0040 | Hypothetical protein, conserved in some lactobacilli | 0 | 3.56E-03 | 2.5 ± 0.5 | ||
LSA0409 | Hypothetical integral membrane protein | 3.02E-05 | 7.25E-03 | 0.61 ± 0.01 | ||
LSA0536 | Hypothetical protein with putative NAD-binding domain, NmrA structural superfamily | 6.28E-06 | 3.32E-02 | 1.6 ± 0.4 | ||
LSA0779 | Hypothetical protein, peptidase S66 superfamily | 4.77E-05 | > threshold | 0.6 ± 0.1 | ||
LSA0991 | Hypothetical protein with putative NAD-binding domain, NmrA structural superfamily | 1.02E-04 | > threshold | 1.6 ± 0.2 | ||
LSA1475 | Hypothetical protein, conserved in bacteria | 1.62-12 | > threshold | 2.1 ± 0.5 | ||
CDS £ | Gene Name | Product | qPCR | |||
LSA0487 | recA | DNA recombinase A | 2.7 ± 0.7 | |||
LSA0992 | dprA | DNA protecting protein, involved in DNA transformation | 2163 ± 1242 |