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Table 3 Genes of the LEE pathogenicity island 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

Z5100

hypothetical protein

1 (20)

−6.8 (0)

−1.5 (1)

−6.8 (0)

−3.2 (2)

1.8 (17)

−6.8 (0)

−1.0 (6)

−3.5 (1)

−6.8 (0)

−6.8 (0)

Z5102

hypothetical protein

1 (149)

−5.5 (2)

−0.7 (15)

−4.9 (4)

−4.1 (7)

0.1 (41)

−8.3 (0)

−0.2 (81)

−4.1 (5)

−3.4 (8)

−8.3 (0)

Z5103

hypothetical protein

1 (128)

−3.0 (10)

−7.9 (0)

−4.0 (7)

−3.0 (15)

1.7 (117)

−7.9 (0)

1.1 (187)

−3.6 (6)

−4.9 (2)

−7.9 (0)

Z5104

hypothetical protein

1 (463)

−3.9 (17)

−3.6 (6)

−2.6 (63)

−2.2 (91)

−0.5 (80)

−3.7 (11)

0.6 (431)

−4.3 (13)

−3.3 (26)

−4.6 (3)

Z5105

secreted protein EspB

1 (903)

−3.5 (46)

−4.6 (6)

−4.5 (35)

−1.5 (302)

−2.0 (57)

−3.8 (21)

0.9 (1070)

−4.3 (26)

−3.1 (55)

−6.8 (1)

Z5106

secreted protein EspD

1 (847)

−4.8 (19)

−5.0 (4)

−6.2 (10)

−2.8 (119)

−0.5 (155)

−4.3 (15)

1.0 (1070)

−4.4 (24)

−3.8 (32)

−12.9 (0)

Z5107

secreted protein EspA

1 (1035)

−4.5 (31)

−7.0 (1)

−7.7 (4)

−2.7 (161)

1.6 (888)

−3.1 (45)

1.4 (1819)

−4.1 (37)

−3.4 (58)

−12.3 (0)

Z5108

hypothetical protein

1 (324)

−4.8 (7)

−5.1 (2)

−11.4 (0)

−3.2 (34)

0.2 (97)

−3.4 (11)

0.8 (347)

−4.5 (8)

−4.0 (12)

−3.0 (7)

Z5109

hypothetical protein

1 (32)

−2.6 (3)

−8.2 (0)

−5.7 (0)

−2.9 (4)

−1.0 (4)

−0.6 (7)

1.4 (52)

−3.0 (2)

−3.3 (2)

−2.3 (1)

Z5110

intimin adherence protein

1 (392)

−4.7 (9)

−4.5 (3)

−5.7 (6)

−3.1 (45)

1.2 (244)

−3.9 (9)

0.6 (376)

−4.6 (9)

−3.4 (20)

−7.3 (0)

Z5111

hypothetical protein

1 (363)

−5.8 (4)

−5.1 (2)

−5.6 (7)

−3.5 (31)

2.6 (608)

−4.7 (5)

1.1 (523)

−4.9 (7)

−3.9 (13)

−10.4 (0)

Z5112

putative translocated intimin receptor protein

1 (247)

−3.4 (15)

−4.4 (2)

−4.8 (8)

−1.8 (67)

1.2 (149)

−2.9 (11)

1.9 (594)

−3.5 (12)

−3.2 (15)

−11.7 (0)

Z5113

hypothetical protein

1 (337)

−3.0 (25)

−2.0 (15)

−2.9 (40)

−1.7 (103)

1.1 (194)

−2.3 (23)

1.7 (689)

−2.5 (36)

−4.2 (10)

−3.3 (6)

Z5114

hypothetical protein

1 (55)

−2.3 (7)

−0.2 (9)

−2.9 (7)

−1.8 (16)

2.7 (102)

−1.3 (8)

2.3 (183)

−2.0 (9)

−3.5 (3)

−7.5 (0)

Z5115

hypothetical protein

1 (111)

−2.9 (10)

−2.0 (5)

−3.6 (8)

−1.9 (30)

1.5 (90)

−1.3 (16)

1.6 (231)

−2.7 (11)

−2.8 (9)

−0.1 (19)

Z5116

hypothetical protein

1 (60)

−2.6 (6)

−2.6 (2)

−5.5 (1)

−2.9 (8)

1.4 (44)

−0.4 (16)

0.8 (71)

−4.1 (2)

−2.1 (9)

0.3 (13)

Z5117

hypothetical protein

1 (53)

−4.1 (2)

−6.9 (0)

−4.4 (2)

−2.7 (7)

1.1 (29)

−2.7 (3)

0.6 (52)

−2.6 (5)

−6.9 (0)

−6.9 (0)

Z5118

hypothetical protein

1 (69)

−4.9 (1)

−2.3 (2)

−7.6 (0)

−4.0 (4)

1.1 (39)

−7.6 (0)

−0.1 (38)

−2.8 (5)

−2.4 (7)

−7.6 (0)

Z5119

hypothetical protein

1 (79)

−2.2 (10)

−3.4 (1)

−3.4 (6)

−2.0 (19)

0.5 (29)

−2.2 (6)

0.8 (84)

−3.7 (4)

−3.7 (4)

−0.9 (7)

Z5120

hypothetical protein

1 (37)

−3.1 (3)

−3.0 (1)

−3.5 (3)

−2.3 (7)

0.7 (17)

−1.5 (4)

1.8 (83)

−2.7 (3)

−3.8 (2)

−9.3 (0)

Z5121

hypothetical protein

1 (29)

−3.8 (1)

−6.5 (0)

−4.0 (1)

−2.0 (8)

2.1 (37)

−1.3 (4)

1.9 (79)

−1.3 (8)

−6.5 (0)

0.9 (10)

Z5122

hypothetical protein

1 (175)

−1.7 (35)

−3.5 (3)

−5.4 (3)

0.5 (245)

3.9 (743)

−0.3 (52)

5.6 (5816)

−1.3 (45)

−4.8 (4)

−2.0 (8)

Z5123

hypothetical protein

1 (41)

−3.4 (2)

−1.8 (2)

−7.1 (0)

−1.7 (11)

2.8 (72)

−1.3 (5)

2.7 (166)

−1.9 (6)

−7.1 (0)

−7.1 (0)

Z5124

hypothetical protein

1 (37)

−3.8 (2)

−7.4 (0)

−4.9 (1)

−1.4 (13)

3.0 (80)

−2.2 (3)

2.2 (106)

−1.2 (9)

−2.5 (4)

−7.4 (0)

Z5125

hypothetical protein

1 (80)

−4.0 (3)

−8.2 (0)

−4.3 (3)

−1.4 (30)

1.8 (75)

−4.0 (2)

1.8 (186)

−2.0 (12)

−4.3 (2)

−2.4 (3)

Z5126

hypothetical protein

1 (50)

−4.4 (1)

−4.0 (1)

−6.8 (0)

−2.4 (9)

2.5 (78)

−1.2 (8)

1.7 (104)

−2.8 (4)

−4.1 (2)

−9.3 (0)

Z5127

hypothetical protein

1 (91)

−4.3 (3)

−8.5 (0)

−8.5 (0)

−2.6 (15)

1.7 (82)

−2.7 (5)

1.2 (143)

−2.5 (10)

−3.6 (5)

−8.5 (0)

Z5128

hypothetical protein

1 (74)

−2.5 (7)

−7.9 (0)

−5.4 (1)

−5.2 (2)

3.1 (165)

−2.2 (5)

−0.1 (44)

−1.6 (15)

−2.7 (6)

−7.9 (0)

Z5129

negative regulator GrlR

1 (118)

−2.4 (14)

−8.5 (0)

−5.1 (3)

−3.9 (7)

3.7 (429)

−0.5 (30)

0.9 (148)

−1.0 (36)

−4.6 (3)

−2.7 (3)

Z5131

hypothetical protein

1 (12)

−5.5 (0)

−5.5 (0)

−2.1 (2)

−2.8 (1)

3.4 (35)

−0.3 (3)

1.0 (16)

−1.2 (3)

−5.5 (0)

1.3 (5)

Z5132

secretion system apparatus protein SsaU

1 (41)

−5.5 (0)

−8.3 (0)

−8.3 (0)

−4.7 (1)

0.1 (11)

−8.3 (0)

−2.5 (4)

−5.0 (1)

−4.3 (1)

−8.3 (0)

Z5133

hypothetical protein

1 (47)

−4.5 (1)

−8.2 (0)

−5.7 (1)

−5.5 (1)

0.2 (15)

−1.7 (5)

−1.9 (8)

−2.7 (4)

−5.2 (1)

−8.2 (0)

Z5134

hypothetical protein

1 (62)

−7.1 (0)

−7.1 (0)

−7.1 (0)

−4.4 (3)

−1.5 (6)

−2.9 (3)

−1.6 (13)

−3.8 (2)

−7.1 (0)

−7.1 (0)

Z5135

type III secretion system protein

1 (95)

−6.2 (1)

−8.9 (0)

−8.9 (0)

−3.6 (7)

0.6 (37)

−2.2 (7)

−1.0 (29)

−4.7 (2)

−5.0 (2)

−8.9 (0)

Z5136

hypothetical protein

1 (149)

−9.5 (0)

−9.5 (0)

−6.1 (2)

−4.3 (7)

−0.3 (32)

−4.3 (2)

−0.7 (56)

−5.2 (2)

−4.0 (5)

−9.5 (0)

Z5137

hypothetical protein

1 (232)

−5.2 (4)

−3.2 (4)

−4.8 (7)

−4.0 (14)

0.5 (84)

−2.8 (11)

−0.8 (84)

−4.1 (8)

−3.1 (15)

−4.3 (2)

Z5138

hypothetical protein

1 (438)

−5.4 (5)

−3.7 (5)

−10.0 (0)

−4.5 (17)

−0.8 (60)

−3.5 (12)

−1.6 (84)

−5.2 (6)

−4.1 (13)

−3.2 (8)

Z5139

hypothetical protein

1 (899)

−6.8 (4)

−10.4 (0)

−10.4 (0)

−5.6 (16)

−1.2 (89)

−2.8 (37)

−2.6 (82)

−5.6 (9)

−5.2 (12)

−3.6 (11)

Z5140

hypothetical protein

1 (597)

−4.0 (23)

−3.2 (11)

−10.9 (0)

−3.1 (67)

0.6 (246)

−1.8 (59)

−0.9 (208)

−4.3 (17)

−4.0 (20)

−3.4 (9)

Z5142

hypothetical protein

1 (51)

−1.8 (9)

−2.0 (2)

−2.8 (6)

−1.0 (23)

−0.1 (12)

−1.6 (6)

1.2 (75)

−2.5 (5)

−2.3 (6)

−1.5 (3)

Z5143

hypothetical protein

1 (6)

−5.2 (0)

−5.2 (0)

−5.2 (0)

−5.2 (0)

−5.2 (0)

−5.2 (0)

1.6 (11)

−5.2 (0)

−5.2 (0)

−5.2 (0)

  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.