Tabulated summary of changes in expression of key genes
| Gene Category and Name) . | Expression in Rb null fetal liver relative to wild type . | Signal Values . | Signal ratio . | P value . | |
|---|---|---|---|---|---|
| Rb−/− . | Wild-type . | ||||
| Hypoxia, Nutrient Deprivation and Oxidative Stress | |||||
| Aldolase A | Increased | 8490.8 | 7189.1 | 1.18 | .001 |
| Phosphoglycerate kinase | Increased | 6100.0 | 4139 | 1.47 | .001 |
| Vascular endothelial growth factor | Increased | 397.9 | 171.5 | 2.32 | .001 |
| Branched chain aminotransferase 2 | Increased | 418.8 | 315.6 | 1.33 | .001 |
| Heme oxygenase | Increased | 4048.1 | 3142.5 | 1.29 | .001 |
| Isocitrate dehydrogenase 2 | Increased | 1285.0 | 889.2 | 1.45 | .026 |
| Fms-like tyrosine kinase 1 | Increased | 225.7 | 181.1 | 1.25 | .002 |
| C/EBP beta | Increased | 804.8 | 573.7 | 1.40 | .001 |
| BNip3 | Increased | 1102.0 | 402.0 | 2.74 | .001 |
| Glutathione peroxidase 3 | Increased | 894.1 | 377.3 | 2.37 | .001 |
| Hexokinase II | Increased | 1392.6 | 620.5 | 2.24 | .001 |
| B-cell translocation gene 1 | Increased | 516.0 | 277 | 1.86 | .001 |
| Macrophage/Dendritic cell lineage | |||||
| Glycoprotein 49 A | Increased | 113.3 | 87.1 | 1.30 | <.001 |
| Lysozyme P | Increased | 616.1 | 340.0 | 1.81 | <.001 |
| Lysozyme M | Increased | 651.3 | 457.2 | 1.42 | <.001 |
| Cathepsin S | Increased | 722.9 | 561.4 | 1.29 | .026 |
| Natural resistance-associated macrophage protein 1 | NC | 989.6 | 1268.2 | 0.78 | .653 |
| CD68 | NC | 374.2 | 314.5 | 1.19 | .166 |
| Complement component 1, q subcomponent, alpha | NC | 418.6 | 367.7 | 1.14 | .268 |
| Complement component 1, q subcomponent, beta | NC | 639.8 | 575.0 | 1.11 | .128 |
| Complement component 1, q subcomponent, c chain | NC | 1070.3 | 1111.1 | 0.92 | .76 |
| TRYO | NC | 506.2 | 552.4 | 0.92 | .187 |
| PU.1 targets | |||||
| Neutrophil elastase | NC | 250.2 | 256.8 | 0.97 | .438 |
| Myeloperoxidase | NC | 1923.5 | 1555.6 | 1.24 | .210 |
| Proteinase 3 | NC | 560.8 | 499.8 | 1.12 | .298 |
| Colony stimulating factor 1 receptor | NC | 597.6 | 475.1 | 1.26 | .084 |
| Gene Category and Name) . | Expression in Rb null fetal liver relative to wild type . | Signal Values . | Signal ratio . | P value . | |
|---|---|---|---|---|---|
| Rb−/− . | Wild-type . | ||||
| Hypoxia, Nutrient Deprivation and Oxidative Stress | |||||
| Aldolase A | Increased | 8490.8 | 7189.1 | 1.18 | .001 |
| Phosphoglycerate kinase | Increased | 6100.0 | 4139 | 1.47 | .001 |
| Vascular endothelial growth factor | Increased | 397.9 | 171.5 | 2.32 | .001 |
| Branched chain aminotransferase 2 | Increased | 418.8 | 315.6 | 1.33 | .001 |
| Heme oxygenase | Increased | 4048.1 | 3142.5 | 1.29 | .001 |
| Isocitrate dehydrogenase 2 | Increased | 1285.0 | 889.2 | 1.45 | .026 |
| Fms-like tyrosine kinase 1 | Increased | 225.7 | 181.1 | 1.25 | .002 |
| C/EBP beta | Increased | 804.8 | 573.7 | 1.40 | .001 |
| BNip3 | Increased | 1102.0 | 402.0 | 2.74 | .001 |
| Glutathione peroxidase 3 | Increased | 894.1 | 377.3 | 2.37 | .001 |
| Hexokinase II | Increased | 1392.6 | 620.5 | 2.24 | .001 |
| B-cell translocation gene 1 | Increased | 516.0 | 277 | 1.86 | .001 |
| Macrophage/Dendritic cell lineage | |||||
| Glycoprotein 49 A | Increased | 113.3 | 87.1 | 1.30 | <.001 |
| Lysozyme P | Increased | 616.1 | 340.0 | 1.81 | <.001 |
| Lysozyme M | Increased | 651.3 | 457.2 | 1.42 | <.001 |
| Cathepsin S | Increased | 722.9 | 561.4 | 1.29 | .026 |
| Natural resistance-associated macrophage protein 1 | NC | 989.6 | 1268.2 | 0.78 | .653 |
| CD68 | NC | 374.2 | 314.5 | 1.19 | .166 |
| Complement component 1, q subcomponent, alpha | NC | 418.6 | 367.7 | 1.14 | .268 |
| Complement component 1, q subcomponent, beta | NC | 639.8 | 575.0 | 1.11 | .128 |
| Complement component 1, q subcomponent, c chain | NC | 1070.3 | 1111.1 | 0.92 | .76 |
| TRYO | NC | 506.2 | 552.4 | 0.92 | .187 |
| PU.1 targets | |||||
| Neutrophil elastase | NC | 250.2 | 256.8 | 0.97 | .438 |
| Myeloperoxidase | NC | 1923.5 | 1555.6 | 1.24 | .210 |
| Proteinase 3 | NC | 560.8 | 499.8 | 1.12 | .298 |
| Colony stimulating factor 1 receptor | NC | 597.6 | 475.1 | 1.26 | .084 |
Data are derived from microarray analyses of mRNA levels between wild-type and Rb−/− fetal liver at E12.5. The average signal values for Rb-null and wild-type samples is given, as is the signal ratio for each gene and the P value to indicate the significance of the change across 9 different sample comparisons (3Rbx3Wt fetal livers). The full array is accessible using the NCBI GEO Series accession number GSE6787.
Phosphoglycerate kinase is commonly abbreviated as pgk1; Vascular endothelial growth factor, as Vegf; Heme oxygenase, as Hmox1; Fms-like tyrosine kinase 1, as flt 1; hexokinase II, as HK2; myeloperoxidase, as MPO; and colony stimulating factor 1 receptor, as c-Fms.