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Table 6 Pathways with cluster assignment articulating tumor versus normal status in at least one PDM layer for the Singh prostate data.

From: Partition decoupling for multi-gene analysis of gene expression profiling data

   

Layer 1

Layer 2

 
 

KEGG Pathway

L p

p ( χ 2 )

f rand

p ( χ 2 )

f rand

In[29]?

00220

Urea cycle & metabolism of amino groups

33

1.14e-13

< 0.001

7.10e-01

0.940

[19, 38, 39]

00980

Metab. of xenobiotics by cytochrome P450

72

3.97e-13

0.001

  

--

00640

Propanoate metabolism

31

7.78e-12

0.003

9.78e-01

0.995

[38, 39]

04610

Complement and coagulation cascades

75

9.21e-12

0.008

2.47e-02

0.371

 

00120

Bile acid biosynthesis

32

1.29e-01

0.699

1.15e-11

0.003

[19, 38]

05060

Prion disease

18

5.18e-02

0.527

2.20e-11

0.003

[19, 38, 39]

00380

Tryptophan metabolism

50

3.84e-11

0.008

5.52e-01

0.894

[39]

00480

Glutathione metabolism

48

4.80e-11

0.008

8.37e-01

0.955

[19, 38, 39]

04310

Wnt signaling pathway

191

5.38e-11

0.017

5.47e-01

0.916

[38]

00983

Drug metabolism - other enzymes

52

5.08e-10

0.024

8.60e-01

0.966

--

04630

Jak-STAT signaling pathway

205

1.65e-01

0.826

8.41e-10

0.025

 

00053

Ascorbate and aldarate metabolism

8

3.32e-02

0.462

7.67e-09

0.008

[39]

00350

Tyrosine metabolism

45

1.32e-02

0.359

2.80e-08

0.040

[19, 38]

00641

3-Chloroacrylic acid degradation

16

5.23e-08

0.016

6.89e-01

0.893

 

00960

Alkaloid biosynthesis II

8

7.13e-02

0.558

8.23e-08

0.016

[19]

00410

beta-Alanine metabolism

25

9.24e-08

0.016

1.60e-01

0.673

[39]

00650

Butanoate metabolism

37

9.39e-02

0.645

1.50e-07

0.014

 

00260

Glycine, serine & threonine metabolism

36

9.56e-02

0.645

1.78e-07

0.014

[38, 39]

00600

Glycosphingolipid metabolism

32

7.84e-02

0.615

3.08e-07

0.016

[19]

00030

Pentose phosphate pathway

21

3.59e-07

0.022

2.80e-01

0.755

[38, 39]

00062

Fatty acid elongation in mitochondria

11

1.68e-01

0.684

3.67e-07

0.022

[19, 38]

00272

Cysteine metabolism

10

6.01e-07

0.025

7.52e-02

0.574

--

00340

Histidine metabolism

27

3.94e-02

0.477

1.42e-06

0.022

[39]

00720

Reductive carboxylate cycle

9

7.62e-02

0.574

1.51e-06

0.025

[19]

00565

Ether lipid metabolism

23

4.07e-06

0.036

8.43e-01

0.948

--

01032

Glycan structures - degradation

39

8.17e-01

0.957

4.62e-06

0.038

 

00360

Phenylalanine metabolism

19

2.32e-02

0.376

6.26e-06

0.044

[38, 39]

00040

Pentose and glucuronate interconversions

17

7.75e-06

0.047

4.98e-01

0.843

[19]

00051

Fructose and mannose metabolism

35

4.49e-03

0.211

7.99e-06

0.043

[19, 38]

  1. The L p column lists the size of the pathway. χ2 test p-values for tumor status versus cluster assignment in PDM layer 1 and layer 2 are given. The frand columns show the fraction of randomly-generated pathways with smaller χ2 p-values in either PDM layer. The final column lists the data sets for which [29] identified the pathway as significant ([19], Singh; [38], Welsh; [39], Ernst; a dash indicates pathways with significant revisions (> 30% of genes added or removed) in KEGG between this analysis and the time of [29] publication).
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BMC Bioinformatics

ISSN: 1471-2105

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