Franny Jongbloed

212 CHAPTER 8 Table 4A. Pathway analysis in female kidney tissue Ingenuity Canonical Pathways Ratio Up/ Down P- value Z-score eIF2 Signaling 9/221 (4.1%) 9/0 6.50 E -04 2,449 Primary Immunodeficiency Signaling 4/48 (8.3%) 0/4 1.72 E -03 N/A Interferon Signaling 3/36 (8.3%) 0/3 6.65 E -03 N/A Complement System 3/37 (8.1%) 0/3 7.18 E -03 N/A Aldosterone Signaling in Epithelial Cells 6/166 (3.6%) 5/1 9.03 E -03 N/A Autoimmune Thyroid Disease Signaling 3/47 (6.4%) 0/3 1.39 E -02 N/A Hematopoiesis from Pluripotent Stem Cells 3/47 (6.4%) 0/3 1.39 E -02 N/A Communication between Innate and Adaptive Immune Cells 4/89 (4.5%) 0/4 1.53 E -02 N/A Cell Cycle: G2/M DNA Damage Checkpoint Regulation 3/49 (6.1%) 2/1 1.55 E -02 N/A NRF2-mediated Oxidative Stress Response 6/193 (3.1%) 6/0 1.79 E -02 N/A Asparagine Degradation I 1/2 (50.0%) 0/1 2.13 E -02 N/A β-alanine Degradation I 1/2 (50.0%) 0/1 2.13 E -02 N/A Proline Degradation 1/2 (50.0%) 0/1 2.13 E -02 N/A Alanine Degradation III 1/2 (50.0%) 0/1 2.13 E -02 N/A Alanine Biosynthesis II 1/2 (50.0%) 0/1 2.13 E -02 N/A A. The top 15 overrepresented pathways derived from the differentially expressed transcripts (DET) in the CCPR diet compared to the control group in kidney tissue of female donors. The pathways show their corresponding ratio of regulated genes as percentage of total genes in the pathway, the E -value and the Z-score for predicted activation or inhibition of the pathways. Significantly activated pathway is depicted in bold. Table 4B. Upstream transcription factor analysis in female kidney tissue Upstream regulator Description Z-score P- value Gene log ratio MYCN MYCN proto-oncogene, bHLH transcription factor +2.985 8.83 E -04 -0.102 MYC MYCN proto-oncogene, bHLH transcription factor +2.191 1.00 E -00 -0.325 NKX2-3 NK2 homeobox 3 +2.000 2.07 E -01 0.197 NKFBIA NFκB inhibitor alpha +1.492 4.64 E -02 -0.349 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 +0.600 1.44 E -02 -0.387 MITF Melanogenesis associated transcription factor + 0.447 4.31 E -02 0.322 STAT3 Signal transducer and activator of transcription 3 + 0.391 7.60 E -04 -0.433 PITX2 Paired like homeodomain 2 + 1.065 2.23 E -03 -0.065 SATB1 SATB homeobox 1 +0.128 8.67 E -03 0.365 WT1 Wilms tumor 1 + 0.101 4.24 E -02 0.265 HNF4A Hepatocyte nuclear factor 4 alpha -0.315 7.41 E -03 -0.239