Table 4:
Gene ontology analysis of genes with significantly altered expression in sham kidneys compared to naïve
| Term | # Genes Represented | Fold Enrichment | FDR |
|---|---|---|---|
| Biological Processes up-regulated in Sham vs naïve: 255 known genes | |||
| cellular response to chemical stimulus (GO:0070887) | 41 | 2.82 | 1.57E-05 |
| response to chemical (GO:0042221) | 51 | 2.28 | 0.000218 |
| transmembrane transport (GO:0055085) | 32 | 3.03 | 0.000224 |
| inflammatory response (GO:0006954) | 15 | 6.2 | 0.000289 |
| response to stimulus (GO:0050896) | 88 | 1.71 | 0.000365 |
| anion transport (GO:0006820) | 18 | 4.63 | 0.000893 |
| ion transport (GO:0006811) | 30 | 2.91 | 0.00149 |
| cell chemotaxis (GO:0060326) | 11 | 8.05 | 0.00169 |
| organic acid metabolic process (GO:0006082) | 23 | 3.51 | 0.00191 |
| response to external stimulus (GO:0009605) | 29 | 2.86 | 0.00342 |
| response to wounding (GO:0009611) | 12 | 6.41 | 0.00474 |
| neutrophil chemotaxis (GO:0030593) | 7 | 15.13 | 0.00586 |
| anion transmembrane transport (GO:0098656) | 12 | 6.24 | 0.00625 |
| response to organic substance (GO:0010033) | 35 | 2.5 | 0.00682 |
| carboxylic acid metabolic process (GO:0019752) | 21 | 3.44 | 0.00867 |
| localization (GO:0051179) | 63 | 1.83 | 0.00937 |
| neutrophil migration (GO:1990266) | 7 | 13.87 | 0.00991 |
| granulocyte chemotaxis (GO:0071621) | 7 | 13.59 | 0.0112 |
| monocarboxylic acid metabolic process (GO:0032787) | 14 | 4.91 | 0.0116 |
| leukocyte chemotaxis (GO:0030595) | 8 | 10.15 | 0.0152 |
| defense response (GO:0006952) | 21 | 3.3 | 0.0165 |
| Biological Processes down-regulated in Sham vs naïve: 130 known genes | |||
| lipid transport (GO:0006869) | 9 | 14.98 | 7.89E-05 |
| lipid localization (GO:0010876) | 9 | 13.7 | 1.65E-04 |
| cholesterol homeostasis (GO:0042632) | 5 | 40.95 | 1.60E-03 |
| cholesterol transport (GO:0030301) | 5 | 38.85 | 2.03E-03 |
| sterol transport (GO:0015918) | 5 | 37.88 | 2.28E-03 |
| sterol homeostasis (GO:0055092) | 5 | 36.07 | 2.85E-03 |
| cholesterol efflux (GO:0033344) | 4 | 67.34 | 4.67E-03 |
| regulation of cholesterol transport (GO:0032374) | 4 | 55.09 | 9.44E-03 |
| regulation of sterol transport (GO:0032371) | 4 | 55.09 | 9.44E-03 |
| very-low-density lipoprotein particle remodeling (GO:0034372) | 3 | > 100 | 1.17E-02 |
| lipid homeostasis (GO:0055088) | 5 | 24.44 | 1.71E-02 |
| organic substance transport (GO:0071702) | 15 | 4.04 | 2.18E-02 |
| triglyceride-rich lipoprotein particle remodeling (GO:0034370) | 3 | > 100 | 2.50E-02 |
| reverse cholesterol transport (GO:0043691) | 3 | > 100 | 4.56E-02 |
| organic hydroxy compound transport (GO:0015850) | 5 | 19.42 | 4.92E-02 |
Gene ontology analysis (Panther over-representation, Fisher’s Exact Test with FDR correction) of kidney gene expression showed that sham kidneys (n=6) significantly upregulated genes involved in an inflammatory response when compared to naïve (n=12). 255 known genes showed >2-fold increase in expression in sham vs naive, FDR<0.05. 130 known genes showed >2-fold decrease in expression in sham compared to naive, FDR<0.05, with enrichment for chemical transport and homeostasis.