Table 3.
Top five enrichments of functional categories of tags consistently and significantly differentially expressed among all three biological replicates and between stages of prostate cancer*
| Top 5 GO † categories | P-value ‡ | Top 5 KEGG § annotations | P-value II | Top 5 SwissProt annotations | P-value II |
|---|---|---|---|---|---|
| AS vs. RAD: Up in RAD¶ | |||||
| Cell communication | 2.E-02 | Stilbene, coumarine and lignin biosynthesis | 1.E-02 | Antioxidant | 7.E-04 |
| Extracellular | 2.E-02 | Butanoate metabolism | 2.E-02 | Cell adhesion | 5.E-03 |
| Extracellular matrix | 2.E-02 | 2,4-Dichlorobenzoate degradation | 2.E-02 | Signal | 6.E-03 |
| Synaptic vesicle transport | 3.E-02 | Cell adhesion molecules (CAMs) | 2.E-02 | Fertilization | 7.E-03 |
| Synapse | 4.E-02 | Alkaloid biosynthesis II | 5.E-02 | Amyotrophic lateral sclerosis | 7.E-03 |
| AS vs. RAD: Down in RAD | |||||
| Glycolysis | 3.E-05 | Glycolysis/Gluconeogenesis | 3.E-05 | Glycolysis | 3.E-07 |
| Glucose catabolism | 1.E-04 | Ribosome | 2.E-03 | Pyrrolidone carboxylic acid | 8.E-05 |
| Hexose catabolism | 1.E-04 | Carbon fixation | 3.E-03 | Pyridoxal phosphate | 2.E-04 |
| Hexose metabolism | 2.E-04 | Fructose and mannose metabolism | 2.E-02 | Gluconeogenesis | 3.E-04 |
| Monosaccharide catabolism | 2.E-04 | Urea cycle and metabolism of amino groups | 3.E-02 | Coiled coil | 5.E-03 |
| RAD vs. CR: Up in CR | |||||
| Acid phosphatase activity | 4.E-02 | gamma-Hexachlorocyclohexane degradation | 5.E-03 | Lyase | 2.E-03 |
| Lyase activity** | 7.E-02 | Glycolysis/Gluconeogenesis | 3.E-02 | Immune response | 5.E-03 |
| Carbohydrate metabolism** | 9.E-02 | O-Glycan biosynthesis | 5.E-02 | Signal | 6.E-03 |
| Extracellular** | 1.E-01 | Ether lipid metabolism** | 6.E-02 | Glycolysis | 7.E-03 |
| Catabolism** | 1.E-01 | Phenylalanine, tyrosine and tryptophan biosynthesis** | 6.E-02 | Progressive external ophthalmoplegia | 1.E-02 |
| RAD vs. CR: Down in CR | |||||
| Cytosolic ribosome | 2.E-09 | Ribosome | 2.E-11 | Ribosomal protein | 6.E-10 |
| Large ribosomal subunit | 1.E-07 | Urea cycle and metabolism of amino groups | 1.E-02 | Ribonucleoprotein | 3.E-08 |
| Cytosol | 2.E-07 | Arginine and proline metabolism | 4.E-02 | Acetylation | 1.E-05 |
| Cytosolic large ribosomal subunit | 2.E-07 | Type II diabetes mellitus** | 1.E-01 | Elongation factor | 1.E-03 |
| Protein biosynthesis | 2.E-07 | Phenylalanine metabolism** | 1.E-01 | rRNA-binding | 2.E-03 |
| AS vs. CR: Up in CR | |||||
| Synapse | 4.E-03 | Butanoate metabolism | 2.E-03 | Glycoprotein | 2.E-03 |
| Extracellular | 5.E-03 | Ascorbate and aldarate metabolism | 2.E-02 | Vitamin C | 7.E-03 |
| Transition metal ion binding | 7.E-03 | Phenylalanine metabolism | 2.E-02 | Lipoprotein | 1.E-02 |
| Metal ion binding | 2.E-02 | Linoleic acid metabolism | 2.E-02 | Signal | 1.E-02 |
| Extracellular matrix | 2.E-02 | gamma-Hexachlorocyclohexane degradation | 2.E-02 | Heparin-binding | 1.E-02 |
| AS vs. CR: Down in CR | |||||
| Cytosolic ribosome | 4.E-12 | Ribosome | 2.E-09 | Acetylation | 2.E-07 |
| Biosynthesis | 7.E-11 | Carbon fixation | 9.E-04 | Ribosomal protein | 1.E-06 |
| Macromolecule biosynthesis | 2.E-10 | Glycolysis/Gluconeogenesis | 3.E-03 | Glycolysis | 7.E-05 |
| Protein biosynthesis | 1.E-08 | Glycosphingolipid biosynthesis - lactoseries | 4.E-02 | Ribonucleoprotein | 8.E-05 |
| Eukaryotic 43 S preinitiation complex | 2.E-08 | Glutamate metabolism** | 8.E-02 | Protein biosynthesis | 1.E-04 |
* Statistics according to the Audic and Claverie test statistic (p ≤ 0.05)
† GO, Gene Ontology
‡ P-value represents the raw EASE (Expression Analysis Systematic Explorer) score
§ KEGG, Kyoto Encyclopedia of Genes and Genomes
II Unadjusted p-value was computed using FatiGO
¶ AS, androgen-sensitive; RAD, responsive to androgen-deprivation; CR, castration-recurrent
** Not statistically significant (p > 0.05)