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Table 2 Functional categories of genes that significantly contribute to PC1 and PC2.

From: Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

Function

P value

Screened members

Total members

Gene names

PC 1 top 5%

    

Galactitol metabolic process

5.98E-06

4

4

gatB, gatC, gatY, gatZ

Phosphate transport

3.58E-07

6

8

phoB, phoU, pstA, pstB, pstC, pstS

Phosphoenolpyruvate-dependent sugar phosphotransferase system

3.01E-04

6

20

dhaH, gatB, gatC, manX, manY, manZ

Response to stress

9.57E-06

13

64

clpB, degP, dnaK, grpE, hslJ, hslU, htpG, ldhA, pstS, uspG, relB, relE, yfiA

Response to heat

1.16E-05

8

24

dnaK, groL, groS, grpE, hslJ, hslU, htpG, ldhA

Protein folding

1.64E-05

8

25

degP, dnaK, dsbA, groS, groL, grpE, htpG, ppiA

PC 1 bottom 5%

    

Cellular amino acid biosynthetic process

3.73E-08

20

100

argF, argI, aroF, aroM, carA, carB, hisA, hisB, hisC, hisD, hisF, hisG, hisH, hisI, leuL, lysC, metH, pheA, thrL, trpL

Histidine biosynthetic process

4.53E-09

8

11

hisA, hisB, hisC, hisD, hisF, hisG, hisH, hisI

Arginine biosynthetic process

3.00E-03

4

13

argF, argI, carA, carB

Tricarboxylic acid cycle

4.05E-04

6

21

fumA, mqo, sdhA, sdhB, sdhC, sdhD

Transport

1.21E-04

33

351

amtB, argT, betT, emrA, entD, fadL, fiu, kgtP, livF, livG, livH, livJ, livK, livM, modA, modB, ompF, oppA, oppB, oppC, oppD, oppF, proP, putP, rbsB, rfbX, sdhA, sdhB, sdhC, sdhD, tsx, uraA, yhbE

Amino acid transport

1.63E-03

8

46

putP, argT, livF, livG, livM, livH, livK, livJ,

Peptide transport

1.91E-03

5

19

oppA, oppB, oppC, oppD, oppF

Flagellum organization

4.72E-04

3

4

flgC, flgD, flhM

PC 2 top 5%

    

Cellular amino acid biosynthetic process

1.49E-10

23

100

argH, aroF, carB, hisB, hisC, hisD, hisH, ilvA, ilvB, ilvC, ilvD, ilvE, ilvM, leuA, leuB, leuC, leuD, trpB, trpC, trpD, trpE, trpL, tyrA

Histidine biosynthetic process

1.50E-03

4

11

hisB, hisC, hisD, hisH

Tryptophan biosynthetic process

1.67E-06

5

6

trpB, trpC, trpD, trpE, trpL

Branched-chain family amino acid biosynthetic process

9.76E-10

10

17

ilvA, ilvB, ilvC, ilvD, ilvE, ilvM, leuA, leuB, leuC, leuD

Iron ion transport

5.47E-17

18

30

cirA, entA, entB, entC, entD, entE, entF, fecA, fecB, fecI, fecR, fepA, fepB, fepC, fes, fhuE, fiu, mntH

Enterobactin biosynthetic process

6.62E-10

7

7

entA, entB, entC, entD, entE, entF, ybdB

Iron-sulfur cluster assembly

1.05E-04

5

11

hscA, iscS, sufA, sufB, sufD

PC 2 bottom 5%

    

Lipopolysaccharide biosynthetic process

2.70E-06

12

49

eptB, kdtA, htrL, rfaB, rfaC, rfaF, rfaG, rfaI, rfaP, rfaQ, rfaS, rfaY

Dipeptide transport

8.29E-05

4

6

dppB, dppC, dppD, dppF