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)

Romanuik et al. BMC Medical Genomics 2010 3:43   doi:10.1186/1755-8794-3-43

Open Data