Skip to main content

Table 4 Genes compared to LB with high logFCs in feces 1

From: Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces

Gene tag

Product

LB

LB-pH9

LB-pH4

LB-15°C

LB-nitrite

LB-antibiotics

LB-solid

minimal medium

spinach juice

radish sprouts

feces

Z0014

molecular chaperone DnaK

1 (185)

−1.0 (55)

0.1 (33)

1.6 (470)

1.6 (520)

0.5 (70)

0.8 (109)

0.0 (120)

3.6 (1290)

1.2 (248)

3.7 (398)

Z0015

chaperone protein DnaJ

1 (74)

−1.4 (16)

−1.4 (4)

1.3 (150)

0.8 (120)

−0.9 (10)

0.0 (23)

−0.5 (31)

0.9 (78)

1.2 (99)

4.2 (220)

Z0045

crotonobetainyl-CoA dehydrogenase

1 (7)

1.3 (10)

0.4 (1)

−0.1 (5)

0.9 (12)

0.7 (3)

2.7 (14)

1.2 (9)

2.5 (23)

−1.5 (1)

5.8 (63)

Z2477

thiosulfate:cyanide sulfurtransferase

1 (558)

0.4 (470)

−0.1 (94)

0.9 (963)

0.1 (603)

−2.3 (31)

−0.7 (121)

−2.2 (83)

−1.6 (113)

−0.4 (252)

2.4 (537)

Z2478

peripheral inner membrane phage-shock protein

1 (17)

1.4 (28)

−4.9 (0)

2.0 (60)

1.2 (37)

−4.9 (0)

1.6 (17)

0.6 (16)

0.6 (15)

4.3 (198)

7.7 (598)

Z2479

DNA-binding transcriptional activator PspC

1 (17)

1.5 (31)

−0.4 (2)

1.9 (57)

1.4 (46)

−0.1 (5)

−5.7 (0)

0.8 (20)

−0.9 (6)

4.1 (182)

7.2 (470)

Z2480

phage shock protein B

1 (25)

1.4 (39)

−0.2 (4)

1.9 (80)

1.2 (55)

−5.5 (0)

−0.3 (7)

−0.9 (8)

0.0 (15)

3.9 (228)

6.8 (482)

Z2482

phage shock protein PspA

1 (64)

0.8 (63)

0.8 (18)

2.0 (206)

0.5 (81)

−0.4 (12)

0.6 (31)

0.6 (59)

0.6 (56)

4.8 (1077)

6.5 (970)

Z2611

DNA replication terminus site-binding protein Tus

1 (9)

−0.4 (4)

1.3 (4)

1.8 (26)

0.8 (15)

−6.0 (0)

0.2 (3)

−1.4 (2)

−1.2 (2)

0.7 (9)

5.0 (47)

Z2876

heat shock protein HtpX

1 (93)

1.4 (154)

0.2 (19)

1.8 (284)

1.0 (187)

−0.2 (22)

3.0 (262)

0.0 (60)

−0.3 (46)

0.1 (59)

3.9 (246)

Z2900

DNA damage-inducible protein YebG

1 (112)

−0.1 (61)

1.3 (42)

−0.1 (83)

0.3 (123)

2.8 (196)

0.8 (59)

0.6 (99)

0.0 (60)

0.8 (113)

3.7 (226)

Z3886

protein disaggregation chaperone ClpB

1 (239)

−1.6 (44)

2.4 (194)

0.5 (267)

0.3 (265)

−0.1 (56)

0.9 (140)

−0.4 (106)

2.7 (827)

1.1 (292)

2.5 (216)

Z4227

isopentenyl-diphosphate delta-isomerase

1 (22)

1.9 (52)

0.3 (5)

1.2 (43)

2.0 (89)

−6.6 (0)

1.2 (18)

0.2 (16)

1.6 (40)

1.5 (38)

5.6 (180)

Z4291

16S ribosomal RNA methyltransferase RsmE

1 (57)

−1.0 (17)

1.0 (18)

−0.9 (26)

−0.8 (30)

0.9 (27)

−1.4 (7)

−0.1 (33)

1.1 (70)

0.0 (34)

4.1 (165)

Z4401

glycogen synthesis protein GlgS

1 (240)

0.4 (182)

−0.2 (32)

−0.4 (141)

1.2 (480)

−0.3 (47)

4.0 (1226)

0.5 (196)

−0.3 (104)

2.6 (838)

6.6 (3617)

Z5182

heat shock chaperone IbpB

1 (26)

−0.2 (13)

−0.1 (4)

0.4 (29)

0.3 (29)

1.5 (19)

2.5 (47)

−0.3 (13)

1.0 (30)

2.4 (80)

5.7 (224)

Z5183

heat shock protein IbpA

1 (26)

0.5 (22)

1.7 (14)

2.1 (96)

1.2 (55)

1.5 (20)

2.6 (54)

0.1 (17)

3.0 (125)

2.2 (72)

6.9 (509)

Z5458

periplasmic repressor CpxP

1 (25)

3.2 (127)

1.7 (13)

0.0 (20)

1.1 (47)

2.9 (45)

4.6 (191)

−0.2 (13)

−2.3 (3)

2.5 (84)

6.0 (260)

  1. 1For each gene, the first number indicates the logFC of a certain condition compared to LB; RPKM values are shown in parentheses. Significantly differentially expressed genes are in bold (i.e., p values ≤ 0.05 in edgeR). For a graphic version, indicating the magnitude of the absolute value of logFC in shades of grey, see Additional file 4.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us