Franny Jongbloed

126 CHAPTER 5 Table 1. Overview of the top overrepresented activated and inhibited canonical pathways after each amino acid-free diet ranked by their –log P- value Canonical Pathway Pathway Classification P- value Genes Ratio Z-score Methionine-free LXR/RXR Activation Nuclear Receptor Signaling 3.24 E -02 6/121 (5%) -2.236 LPS/IL-1 Mediated Inhibition of RXR Function Nuclear Receptor Signaling 5.61 E -10 22/222 (10.0%) -1.897 Antioxidant Action of Vitamin C Cellular Stress and Injury 1.61 E -02 6/103 (5.8%) -1.000 PPARa/RXRa Activation Nuclear Receptor Signaling 8.78 E -03 9/178 (5.1%) +0.378 eNOS Signaling Cardiovascular Signaling 3.37 E -02 7/155 (4.5%) +0.447 ERK5 Signaling Intracellular and Second Messenger Signaling 3.53 E -02 4/63 (6.3%) +1.000 CNTF Signaling Cytokine Signaling/ Neurotransmitters and Other Nervous System Signaling/ Cellular Growth 3.53 E -02 4/63 (6.3%) +1.000 UVA-Induced MAPK Signaling Cellular Stress and Injury 1.54 E -02 6/102 (5.9%) +1.000 Cell Cycle: G2/M DNA Damage Checkpoint Regulation Cell Cycle Regulation 2.68 E -03 5/49 (10.2%) +1.342 Melanocyte Development and Pigmentation Signaling Growth Factor Signaling 3.94 E -02 5/95 (5.3%) +2.000 NRF2-mediated Oxidative Stress Response Cellular Stress and Injury 1.54 E -07 18/193 (9.3%) +2.646 Leucine-Free NRF2-mediated Odixative Stress Response Cellular Stress and Injury 3.46 E -05 18/193 (9.3%) +2.309 Calcium-induced T-lymphocyte Apoptosis Apoptosis/Cellular Immune Response 1.94 E -04 9/66 (13.6%) +1.000 LPS/IL-1 Mediated Inhibition of RXR Function Nuclear Receptor Signaling 2.09 E -04 18/222 (8.1%) -0.816 Role of NFAT in Regulation of the Immune Response Intracellular and Second Messenger Signaling 6.87 E -04 15/185 (8.1%) +1.069 Cholecystokinin/Gastrin- mediated Signaling Neurotransmitters and Other Nervous System Signaling 1.18 E -03 10/101 (9.9%) +1.265 CD28 Signaling in T Helper Cells Cellular Immune Response 2.61 E -03 11/131 (8.4%) +0.447 PKCo Signaling in T Lymphocytes Cellular Immune Response 2.77 E -03 11/132 (8.3%) +1.508 Tec Kinase Signaling Intracellular and Second Messenger Signaling 6.95 E -03 12/170 (7.1%) +0.333 Phospholipase C Signaling Intracellular and Second Messenger Signaling 7.42 E -03 15/237 (6.3%) +1.291