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Table 1 Genes upregulated at least 2-fold after acid shift.a

From: Rapid acid treatment of Escherichia coli: transcriptomic response and recovery

1 min Log2 ratios Maurer et al 2005b % Recovery 5 min Log2 ratios Maurer et al 2005b % Recovery 10 min Log2 ratios Maurer et al 2005b % Recovery
hisL 2.3   66 yagU 4.3 + 10 cadB 4.7   0
thrL 1.7   77 bdm 4.0   20 yagU 3.8 + 10
b2596 1.6   90 ymgB 3.8   44 glpD 3.7   0
raiA 1.5   46 glpD 3.5   0 glpK 3.5   0
YfiD 1.5 + 52 sra 3.1 + 0 hdeB 3.5 + 0
YifN 1.4   75 cadB 3.1   0 glpF 3.3   0
YifO 1.4   87 ymgA 3.0   38 hdeA 3.3 + 0
evgA 1.3   45 ymgC 2.6   52 sra 3.3 + 0
yhcN 1.3 + 23 yhcN 2.6 + 23 yahO 3.2   0
ymgB 1.3   44 yneI 2.6   57 bdm 3.2   20
uspD 1.2   44 gatB 2.5 + 0 cadA 3.2 + 0
ymgA 1.2   38 raiA 2.5   46 osmY 3.1   0
yagU 1.1 + 10 aceB 2.4   33 gatB 3.1 + 0
pmrD 1.1   68 b2596 2.4   90 lldR 3.1   0
ycgZ 1.0   39 uspD 2.4 + 44 gatC 3.0 +  
     gltA 2.3 + 10 yjbJ 3.0   0
     lldR 2.3   0 lldD 2.9 + 0
     gadE 2.2   15 yhjX 2.8   0
     lldD 2.2 + 0 gatA 2.8 + 0
     osmY 2.2   0 lldP 2.8 + 0
     glpF 2.2   0 rcsA 2.7   0
     ycgZ 2.2   39 yjdL 2.6   0
     osmB 2.2   0 gatZ 2.6 + 0
     rcsA 2.1   0 tnaC 2.5   0
     hdeB 2.1 + 0 glpQ 2.5   0
     gatA 2.1 + 0 clpB 2.4 + 0
     aceA 2.1   8 gcvT 2.4   0
     ygaC 2.1   46 ivy 2.3   0
     ivy 2.0   0 osmB 2.3   0
     yfiD 2.0 + 52 glpT 2.3   0
     yahO 2.0   0 dppF 2.3   0
     gatZ 2.0   0 msyB 2.2   0
     elbA 2.0   59 talA 2.2   0
     yjbJ 1.9   0 yiaG 2.2   0
     lldP 1.9 + 0 gcvH 2.2   0
     hisL 1.9   66 sucD 2.2 + 0
     amn 1.9   27 ymgB 2.1   44
     yeiG 1.9 + 25 gltA 2.1 + 10
     hdeA 1.9 + 0 gatY 2.0   0
     glpK 1.9   0 ydiZ 2.0   0
     gatC 1.8    yeaD 2.0   
     yhjX 1.8   0 yhcN 2.0 + 23
     crl 1.8   64 gadE 1.9   15
     hchA 1.8   27 ygaM 1.9   0
     gadW 1.8   17 aceA 1.9   8
     gltB 1.7    yhcO 1.9   0
     ilvC 1.7   65 dps 1.9 + 0
     arcB 1.7   50 ymgA 1.9   38
     evgA 1.7   45 ygdI 1.8 + 0
     uspA 1.6   60 gadB 1.8   0
     asd 1.6   33 bfr 1.7   0
     ghrB 1.6   24 gltB 1.7   
     osmC 1.6   11 ygiW 1.7 + 0
     cfa 1.6 + 17 sthA 1.7 + 0
     nlpA 1.6 + 51 aceB 1.6   33
     ycgK 1.6   38 yphA 1.6   0
     intA 1.6   77 elaB 1.6   0
     dps 1.6 + 0 yjiT 1.6   0
     rhsA 1.6   30 srlD 1.6 + 0
     fimB 1.6   98 spy 1.6   0
     yieF 1.6 + 0 aldA 1.6 + 0
     fpr 1.6 + 47 yieF 1.6 + 0
     yiiS 1.6 + 23 acs 1.6   0
     yieE 1.5 + 33 manY 1.6   0
     gatY 1.5   0 hdeD 1.6   0
     yhcO 1.5   0 dppA 1.5   0
     yggE 1.5   0 gadA 1.5   0
     insI 1.5   47 yeaG 1.5   0
     clpS 1.5   62 yggE 1.5   0
     glgC 1.5   2 mglB 1.5   0
     ydiZ 1.5   0 yncC 1.5   0
     dtd 1.5   47 b1005 1.5   0
     marA 1.5 + 21 gadW 1.5   17
     sthA 1.4 + 0 ykgA 1.4 + 0
     argE 1.4   57 osmC 1.4   11
     clpB 1.4 + 0 glgC 1.4   2
     serC 1.4 + 57 ytfK 1.4   0
     msyB 1.4 + 0 sdhB 1.4 + 0
     tas 1.4 + 24 dhaM 1.4 + 0
     ygdI 1.4 + 0 yeiG 1.4 + 25
     rsd 1.4   67 manZ 1.4   0
     aroG 1.4   58 ygaU 1.4   0
     bcsE 1.4 + 37 ykgE 1.4   0
     yciI 1.4   74 sdhC 1.4 + 0
     gcvR 1.4   81 dadA 1.4   
     nrdH 1.3   78 amn 1.4   27
     bcsF 1.3   31 yodC 1.4 + 0
     ygdR 1.3   22 manX 1.4   0
     acnB 1.3 + 15 udp 1.4 + 0
     appY 1.3   36 fumA 1.4 + 0
     ypeC 1.3   36 glgS 1.4   0
     yrdA 1.3   29 ycgZ 1.3   39
     hdfR 1.3   73 cfa 1.3 + 17
     yjdJ 1.3   4 ybjP 1.3   0
     thrL 1.3   77 raiA 1.3   46
     umC 1.3   5 oppB 1.3   
     yncC 1.3   0 yehE 1.3   0
     yjiT 1.3   0 uspD 1.3 + 44
     gcvT 1.3   0 mqo 1.3 + 0
     ugpB 1.3   25 oppA 1.3   
     ygbE 1.3 + 1 sdhA 1.3 + 0
     hdfR 1.3   65 hdhA 1.3   0
     hdhA 1.3   0 hchA 1.3   27
     yjgK 1.3 + 41 yhhA 1.3   0
     cadA 1.2 +   dppD 1.3   0
     rpoS 1.2    poxB 1.3   0
     oppB 1.2    srlE 1.3 + 0
     dadA 1.2    yjdI 1.2   0
     oppA 1.2    ygbE 1.2 + 1
     ybjP 1.2   0 ghrB 1.2   24
     sbmC 1.2   47 yjdJ 1.2   4
     malP 1.2   55 ymgC 1.2   52
     msrA 1.2   50 mglA 1.2   0
     bcp 1.2   72 fumC 1.2   5
     arcA 1.2   47 wrbA 1.2   0
     mqo 1.2 + 0 ykgF 1.2   0
     ycbB 1.2   42 yqjD 1.2   0
     yjdL 1.2   0 cdd 1.2 + 0
     yhhA 1.2   0 yiiS 1.2 + 23
     malQ 1.2   58 yqjC 1.2   0
     nadE 1.2 + 39 groL 1.2 + 0
     aldA 1.2 + 0 ygaF 1.2   0
     cyaA 1.2 + 73 otsB 1.2   0
     dkgA 1.2   9 marA 1.1 + 21
     marR 1.2 + 28 htpG 1.1 + 0
     glgS 1.2   0 acnB 1.1 + 15
     yeaR 1.2   11 srlA 1.1 + 0
     gdhA 1.2   54 ybeL 1.1   0
     ykgA 1.2 + 0 ygaC 1.1   46
     yfaO 1.2   34 asd 1.1   33
     soxS 1.2   85 dkgA 1.1   9
     ygiN 1.2   63 rhsA 1.1   30
     fucK_ 1.2   65 ydiH 1.1 + 0
     yodA 1.2   79 dhaK 1.1 + 0
     sucD 1.2 + 0 yneI 1.1   57
     argT 1.2   58 sdhD 1.1 + 0
     ygaM 1.2   0 dhaL 1.1   0
     rhsD 1.2   108 yhdN 1.1   6
     fxsA 1.1    yeaQ 1.1 + 0
     yqhD 1.1    uspB 1.1   0
     yihY 1.1    yeaR 1.1   11
     yhdN 1.1   6 gltD 1.1 + 0
     gloB 1.1   46 tas 1.0 + 24
     hdeD 1.1   0 ygdR 1.0   22
     sdhA 1.1 + 0 sodC 1.0   0
     yiaG 1.1   0 yieE 1.0 + 33
     zntR 1.1   23 galP 1.0   0
     yjeI 1.1   84 fliY 1.0 + 0
     ldhA 1.1   37 nemA 1.0   
     yqhD 1.1   18     
     srlD 1.1 + 0     
     yihY 1.1   18     
     yeaC 1.1 + 19     
     gcvH 1.1   0     
     talA 1.1   0     
     yphA 1.1   0     
     ybaQ 1.1   96     
     nrdI 1.1   80     
     ygiW 1.1 + 0     
     yfjU 1.1   11     
     elaB 1.1   0     
     yjdC 1.1   16     
     yfbU 1.1   46     
     bcsG 1.1   34     
     sdhC 1.1 + 0     
     yohN 1.1 + 11     
     bolA 1.1   65     
     yjdI 1.1   0     
     sdhB 1.1 + 0     
     ydiV 1.1   62     
     mcrB 1.1   15     
     yggG 1.1   18     
     dppA 1.1   0     
     mcrC 1.1   12     
     nemA 1.0       
     yeaD 1.0       
     ygaU 1.0   0     
     yjbQ 1.0 + 55     
     yfbQ 1.0 + 52     
     yihD 1.0   65     
     ybeL 1.0   0     
     phoP 1.0   44     
     nlpD 1.0   20     
     gadB 1.0   0     
     uspB 1.0   0     
     rpoN 1.0   56     
     yfjH 1.0   38     
     yaiB 1.0   8     
     spy 1.0   0     
     betI 1.0   138     
     lrp 1.0   44     
     ybhGt 1.0   74     
     gadX 1.0   23     
     ygiT 1.0   101     
     kch 1.0   47     
     ygdH 1.0   37     
  1. a Values shown represent the log2 ratio of expression indices compared to those at time zero. Expression ratios of 2-fold or greater are shown. Percent recovery is defined under Results; a blank cell indicates recovery could not be defined.
  2. b Ref [11]
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