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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*

From: LNCaP Atlas: Gene expression associated with in vivoprogression to castration-recurrent 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
  1. * Statistics according to the Audic and Claverie test statistic (p ≤ 0.05)
  2. † GO, Gene Ontology
  3. ‡ P-value represents the raw EASE (Expression Analysis Systematic Explorer) score
  4. § KEGG, Kyoto Encyclopedia of Genes and Genomes
  5. II Unadjusted p-value was computed using FatiGO
  6. ¶ AS, androgen-sensitive; RAD, responsive to androgen-deprivation; CR, castration-recurrent
  7. ** Not statistically significant (p > 0.05)