Table 4

Biological processes of differentially expressed genes of each cluster

Classification of clustered genes

Number of genes

Percentage of genes

P value

Cluster 1 (233 differentially expressed genes)

Other metabolism (BP00289)

15

6.70%

8.09 × 10^-5

Carbohydrate metabolism (BP00001)

13

5.80%

0.000695

Cell structure and motility (BP00285)

19

8.50%

0.000846

Transport (BP00141)

21

9.40%

0.003032

Phosphate metabolism (BP00095)

4

1.80%

0.011909

Cell cycle (BP00203)

14

6.30%

0.019047

Protein targeting and localization (BP00137)

5

2.20%

0.023674

Intracellular protein traffic (BP00125)

14

6.30%

0.025339

Cluster 2 (96 differentially expressed genes)

Cell cycle (BP00203)

14

6.30%

3.05 × 10^-6

Cell proliferation and differentiation (BP00224)

9

2.70%

0.004340

Cell adhesion (BP00124)

7

4.00%

0.005309

Cell structure and motility (BP00285)

9

8.50%

0.009058

Oncogenesis (BP00281)

5

0.90%

0.016163

Apoptosis (BP00179)

5

2.20%

0.028634

Homeostasis (BP00267)

3

1.80%

0.034910

Cluster 3 (102 differentially expressed genes)

Amino acid metabolism (BP00013)

6

6.10%

0.0002

Cell adhesion (BP00124)

9

9.20%

0.0004

Cell structure and motility (BP00285)

11

11.20%

0.0012

Lipid, fatty acid, and steroid metabolism (BP00019)

9

9.20%

0.0024

Other metabolism (BP00289)

6

6.10%

0.0172

Oncogenesis (BP00281)

5

5.10%

0.0190

Developmental processes (BP00193)

13

13.30%

0.0475

Cluster 4 (49 differentially expressed genes)

Immunity and defense (BP00148)

9

20.00%

0.0020

Muscle contraction (BP00173)

3

6.70%

0.0030

Nguyen et al. Arthritis Research & Therapy 2009 11:R56   doi:10.1186/ar2676