1. Te Pas et al Additional File 3 Detailed graphical representation of the main pathway results

2. Explanation to read the Figures 1.Circles – denote genes with data on the microarray 2.Boxes – indicate regulated processes / other pathways 3.Colour code No colour: no up or down regulation Green: up regulation Red: down regulation Blue: probably regulated, direction uncertain ExperimentsContent Exp 1Line A: infected versus control Exp 2Line B: infected versus control Exp 3Line A versus Line B: control Exp 4Line A versus Line B: infected

3. Adherens junction Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

4. Adherens junction Line differences control / infected Exp 3: control Exp 4: infected

5. Adipocytokine signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

6. Adipocytokine signaling Line differences control / infected Exp 3: control Exp 4: infected

7. Aminosugars metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

8. Aminosugars metabolism Line differences control / infected Exp 3: control Exp 4: infected

9. Androgen and Estrogen metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

10. Androgen and Estrogen metabolism Line differences control / infected Exp 3: control Exp 4: infected

11. Apoptosis Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

12. Apoptosis Line differences control / infected Exp 3: control Exp 4: infected

13. Beta-Alanine metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

14. Beta-Alanine metabolism Line differences control / infected Exp 3: control Exp 4: infected

15. Arachidonic acid metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

16. Arachidonic acid metabolism Line differences control / infected Exp 3: control Exp 4: infected

17. Axon guidance Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

18. Axon guidance Line differences control / infected Exp 3: control Exp 4: infected

19. B cell receptor signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

20. B cell receptor signaling Line differences control / infected Exp 3: control Exp 4: infected

21. Benzoate degradation via CoA ligation Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

22. Benzoate degradation via CoA ligation Line differences control / infected Exp 3: control Exp 4: infected

23. Bile acid biosynthesis Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

24. Bile acid biosynthesis Line differences control / infected Exp 3: control Exp 4: infected

25. Caprolactam degradation Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

26. Caprolactam degradation Line differences control / infected Exp 3: control Exp 4: infected

27. Cell adhesion molecules Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

28. Cell adhesion molecules Line differences control / infected Exp 3: control Exp 4: infected

29. Cell communication / Cell junction Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

30. Cell communication / Cell junction Line differences control / infected Exp 3: control Exp 4: infected

31. Circadian rhythm Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

32. Circadian rhythm Line differences control / infected Exp 3: control Exp 4: infected

33. Complement and Coagulation cascades Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

34. Complement and Coagulation cascades Line differences control / infected Exp 3: control Exp 4: infected

35. Cytokine-cytokine receptor interaction Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

36. Cytokine-cytokine receptor interaction Line differences control / infected Exp 3: control Exp 4: infected

37. Dorso-ventral axis formation Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

38. Dorso-ventral axis formation Line differences control / infected Exp 3: control Exp 4: infected

39. Fatty acid metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

40. Fatty acid metabolism Line differences control / infected Exp 3: control Exp 4: infected

41. Focal adhesion Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

42. Focal adhesion Line differences control / infected Exp 3: control Exp 4: infected

43. Gap junction Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

44. Gap junction Line differences control / infected Exp 3: control Exp 4: infected

45. Glutatione metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

46. Glutatione metabolism Line differences control / infected Exp 3: control Exp 4: infected

47. Glycerolipid metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

48. Glycerolipid metabolism Line differences control / infected Exp 3: control Exp 4: infected

49. Gly, Ser, Thr metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

50. Gly, Ser, Thr metabolism Line differences control / infected Exp 3: control Exp 4: infected

51. Insulin signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

52. Insulin signaling Line differences control / infected Exp 3: control Exp 4: infected

53. JAK-STAT signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

54. JAK-STAT signaling Line differences control / infected Exp 3: control Exp 4: infected

55. Leukocyte transendothelial migration Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

56. Leukocyte transendothelial migration Line differences control / infected Exp 3: control Exp 4: infected

57. Long-term depression Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

58. Long-term depression Line differences control / infected Exp 3: control Exp 4: infected

59. Long-term potentiation Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

60. Long-term potentiation Line differences control / infected Exp 3: control Exp 4: infected

61. MAPK signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

62. MAPK signaling Line differences control / infected Exp 3: control Exp 4: infected

63. Metabolism of Xenobiotics by cytochrome P450 Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

64. Metabolism of Xenobiotics by cytochrome P450 Line differences control / infected Exp 3: control Exp 4: infected

65. Natural killer cell mediated cytotoxicity Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

66. Natural killer cell mediated cytotoxicity Line differences control / infected Exp 3: control Exp 4: infected

67. N-glycan biosynthesis Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

68. N-glycan biosynthesis Line differences control / infected Exp 3: control Exp 4: infected

69. Pantothenate and CoA biosynthesis Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

70. Pantothenate and CoA biosynthesis Line differences control / infected Exp 3: control Exp 4: infected

71. Pentose phosphate pathway Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

72. Pentose phosphate pathway Line differences control / infected Exp 3: control Exp 4: infected

73. Proteasome Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

74. Proteasome Line differences control / infected Exp 3: control Exp 4: infected

75. Purine metabolism Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

76. Purine metabolism Line differences control / infected Exp 3: control Exp 4: infected

77. Regulation of actin cytoskeleton Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

78. Regulation of actin cytoskeleton Line differences control / infected Exp 3: control Exp 4: infected

79. T cell receptor signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

80. T cell receptor signaling Line differences control / infected Exp 3: control Exp 4: infected

81. TGF-beta signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

82. TGF-beta signaling Line differences control / infected Exp 3: control Exp 4: infected

83. Tight junction Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

84. Tight junction Line differences control / infected Exp 3: control Exp 4: infected

85. Val, Leu and Ile degradation Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

86. Val, Leu and Ile degradation Line differences control / infected Exp 3: control Exp 4: infected

87. WNT signaling Line differences reaction to Salmonella Exp 1: line A Exp 2: line B

88. WNT signaling Line differences control / infected Exp 3: control Exp 4: infected