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Table 3 The most significantly altered pathways in melanoma cells.

From: Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes

Pathway ID

Description

KEGG Category/Description*

# genes

# up-regulated genes

# down-regulated genes

p-value

up-regulated

      

230

Purine metabolism

Nucleotide Metabolism

119

11

23

4.37E-05

440

Aminophosphonate metabolism

Metabolism of Other Amino Acids

12

0

6

0.000153

626

Nitrobenzene degradation

Biodegradation of Xenobiotics

11

0

5

0.00098

363

Bisphenol A degradation

Biodegradation of Xenobiotics

16

0

6

0.00101

350

Tyrosine metabolism

Amino Acid Metabolism

44

6

10

0.00196

450

Selenoamino acid metabolism

Metabolism of Other Amino Acids

20

0

6

0.00370

52

Galactose metabolism

Carbohydrate Metabolism

27

2

7

0.00429

4540

Gap junction

Cell Communication

85

4

14

0.00670

340

Histidine metabolism

Amino Acid Metabolism

31

1

7

0.00964

4110

Cell cycle

Growth and Death

98

2

15

0.01009

Down-regulated

      

190

Oxidative phosphorylation

Energy Metabolism

128

46

8

2.95E-27

193

ATP synthesis

Energy Metabolism

42

14

4

2.68E-08

720

Reductive carboxylate cycle

Energy Metabolism

10

6

0

5.25E-06

20

Citrate cycle (TCA cycle)

Carbohydrate Metabolism

26

9

2

6.56E-06

620

Pyruvate metabolism

Carbohydrate Metabolism

35

8

5

0.00057

240

Pyrimidine metabolism

Nucleotide Metabolism

72

12

12

0.00057

660

C5-branched dibasic acid metabolism

Carbohydrate Metabolism

2

2

0

0.00319

480

Glutathione metabolism

Metabolism of Other Amino Acids/Neutralization of ROS*

37

7

1

0.00400

280

Valine, leucine and isoleucine degradation

Amino Acid Metabolism

39

7

6

0.00543

  1. Pathways with p-values around 0.010 or lower are listed. The most significantly altered pathways (p ≤ 0.005) after being validated with manual curation are shown in bold.