Table 3. Significant differently expressed genes in all Superfund versus all reference site populations.
A gene with a positive fold-difference is more highly expressed in the Superfund populations, and a gene with a negative fold-difference is more highly expressed in the reference populations. P-values for New Bedford Harbor (NBH), Newark Bay (NB) and Elizabeth River (ER) populations versus their respective reference site populations also are reported. Significant p-values for these three separate comparisons are in bold. Gene names in bold are consistently up or down regulated in the all Superfund versus all reference comparison and in each separate comparison, NBH, NB, and ER.
| Gene | Pathway | Function | P-value | Fold Difference | P-value NBH | P-value NB | P-value ER |
|---|---|---|---|---|---|---|---|
| Cytochrome c oxidase subunit VIIIb | Oxidative Phosphorylation | Energy Metabolism | 8.44E-04 | 1.09 | 4.40E-02 | 1.04E-03 | 5.97E-01 |
| ATP synthase H+ transporting mitochondrial F1 complex delta subunit | Oxidative Phosphorylation | 2.06E-03 | 1.06 | 2.19E-01 | 4.61E-02 | 3.15E-01 | |
| ATP synthase H+ transporting mitochondrial F0 complex subunit b isoform 1 | Oxidative Phosphorylation | 3.81E-05 | -1.09 | 4.28E-01 | 1.22E-04 | 7.06E-02 | |
| 6-phosphogluconolactonase | Pentose-phosphate shunt | 6.66E-04 | 1.07 | 1.07E-04 | 5.03E-03 | 7.76E-01 | |
| PEP carboxykinase phosphoenolpyruvate carboxykinase | Carbohydrate biosynthesis | 7.41E-03 | 1.08 | 6.16E-03 | 9.09E-01 | 1.77E-01 | |
| Isocitrate dehydrogenase 1 (cytosolic or soluble IDH1) | Carbohydrate metabolism | 1.42E-03 | -1.11 | 3.28E-01 | 3.52E-01 | 5.29E-03 | |
| Electron transfer flavoprotein beta-subunit | Electron transfer flavoprotein | 1.64E-04 | -1.10 | 2.31E-01 | 3.32E-05 | 8.17E-01 | |
| Acyl-CoA desaturase | Fatty acid desaturase | 3.47E-03 | 1.09 | 2.55E-01 | 1.07E-01 | 7.07E-01 | |
| Phosphoglycerate mutase type B | Glycolysis | 4.27E-04 | 1.10 | 6.55E-01 | 2.00E-01 | 1.46E-02 | |
| Fructose-1,6-bisphosphatase | Glycolysis | 1.36E-06 | -1.16 | 2.96E-04 | 1.04E-03 | 8.19E-02 | |
| 3-ketoacyl-CoA thiolase, mitochondrial | Lipid metabolism; fatty acid metabolism | 1.20E-03 | -1.07 | 1.40E-01 | 5.36E-01 | 1.23E-02 | |
| ADP, ATP carrier protein, isoform T2 | Transport | 3.79E-04 | -1.10 | 1.85E-01 | 1.31E-05 | 9.45E-01 | |
| Phospholipase A2 precursor | Lipid degradation | Catabolism | 3.36E-04 | 1.19 | 2.89E-01 | 6.51E-04 | 1.08E-02 |
| Group XIII secreted phospholipase A2 | Lipid degradation | 3.30E-04 | -1.11 | 8.80E-01 | 5.73E-02 | 6.84E-03 | |
| Isoamyl acetate-hydrolyzing esterase | Probable lipase | 8.28E-04 | 1.06 | 3.41E-03 | 1.13E-01 | 9.06E-01 | |
| 4-hydroxyphenylpyruvate dioxygenase | Tyrosine catabolic process | 1.88E-03 | 1.06 | 9.78E-04 | 5.75E-01 | 9.22E-02 | |
| Delta-5/delta-6 fatty acid desaturase | Biosynthesis of HUFA | Biosynthesis | 1.99E-03 | 1.10 | 1.32E-02 | 3.14E-02 | 8.20E-01 |
| Cystathionine-beta-synthase | Cysteine Metabolic process | 2.95E-04 | -1.11 | 7.71E-01 | 1.67E-01 | 6.41E-05 | |
| Fatty acid synthase | Fatty acid synthesis | 2.49E-07 | 1.31 | 8.50E-04 | 7.11E-01 | 2.77E-01 | |
| 3-oxoacyl-[acyl-carrier protein] reductase | Fatty acid synthesis | 9.22E-04 | 1.09 | 8.18E-04 | 6.37E-01 | 1.17E-01 | |
| Myo-inositol 1-phosphate synthase A1 | Myo-inositol biosynthesis pathway | 1.72E-04 | 1.22 | 8.44E-01 | 8.91E-01 | 2.80E-03 | |
| Ornithine decarboxylase antizyme, short isoform | Polyamine biosynthesis | 1.91E-05 | -1.11 | 2.75E-03 | 9.97E-03 | 9.15E-02 | |
| Elongation factor 1-alpha | Protein synthesis | 2.03E-03 | -1.08 | 8.12E-02 | 3.52E-03 | 5.81E-01 | |
| Cytochrome P450 2N2 | Arachidonic acid metabolism | Regulation/Signaling | 8.00E-03 | -1.13 | 8.22E-03 | 1.04E-02 | 1.99E-05 |
| Fatty acid binding protein H6-isoform | Lipid binding, transporter activity | 7.75E-05 | 1.12 | 9.05E-03 | 1.16E-01 | 2.10E-03 | |
| Troponin I, slow skeletal muscle | Regulation of muscle contraction | 8.41E-04 | -1.12 | 2.54E-02 | 1.44E-05 | 9.84E-02 | |
| Forkhead box P2 | Transcription factor | 8.35E-05 | 1.22 | 3.61E-01 | 3.98E-03 | 6.69E-03 | |
| Basic transcription factor 3 | Transcription factor | 1.01E-05 | 1.11 | 1.77E-02 | 1.97E-02 | 4.92E-01 | |
| Protein disulfide isomerase A3 precursor | Catalyzes the rearrangement of -S-S- bonds in proteins | Other | 1.09E-04 | -1.13 | 6.81E-01 | 1.88E-06 | 3.53E-02 |
| Cytochrome P450 2K2 | Lauric acid hydroxylase | 4.77E-04 | -1.12 | 1.03E-02 | 5.38E-03 | 5.39E-01 | |
| Phosphomannomutase 1 | Mannose metabolic process | 2.70E-04 | 1.21 | 2.37E-01 | 2.18E-03 | 1.40E-02 | |
| Tropomyosin alpha 4 chain | Muscle contraction | 7.15E-04 | 1.10 | 3.88E-02 | 3.25E-01 | 8.98E-03 | |
| Cytokine receptor common gamma chain precursor | Common interleukin receptor subunit | 8.74E-03 | 1.10 | 3.05E-05 | 5.76E-01 | 6.07E-01 |