Table 1

Comparison of Gene Ontology and metabolic pathway enrichment by cluster metric (Euclidean vs Pearson) for medium stringency dataset.

Pearson metric - Cluster 1 d - Biological Process

Genes

% input

P-Value

Benjam


response to wounding

28

10.6

1.7E-15

9.2E-12

acute inflammatory response

17

6.4

2.6E-15

6.9E-12

response to external stimulus

32

12.1

5.6E-14

9.6E-11

inflammatory response

20

7.6

4.3E-11

5.6E-08

acute-phase response

9

3.4

7.8E-10

8.1E-07

response to stress

31

11.7

1.0E-07

9.0E-05

electron transport

22

8.3

2.4E-07

1.7E-04

complement activation

8

3

9.5E-07

6.2E-04

activ of plasma proteins in acute inflam response

8

3

9.5E-07

6.2E-04

complement activation, classical pathway

7

2.7

1.2E-06

6.0E-04

wound healing

10

3.8

1.8E-06

8.5E-04

generation of precursor metabolites and energy

23

8.7

2.3E-06

1.0E-03

humoral immune response by immunoglobulin

7

2.7

3.7E-06

1.5E-03

complement activation, alternative pathway

5

1.9

4.3E-06

1.6E-03

blood coagulation

8

3

8.1E-06

2.8E-03

coagulation

8

3

9.1E-06

2.9E-03

defense response

25

9.5

9.1E-06

2.8E-03

hemostasis

8

3

1.1E-05

3.2E-03

regulation of body fluid levels

8

3

5.0E-05

1.4E-02

activation of immune response

8

3

7.4E-05

1.9E-02

regulation of multicellular organismal process

14

5.3

1.1E-04

2.7E-02

regulation of immune response

9

3.4

1.4E-04

3.3E-02

immune response

19

7.2

1.5E-04

3.4E-02

regulation of immune system process

9

3.4

1.6E-04

3.3E-02

positive reg of multicellular organismal process

9

3.4

2.2E-04

4.4E-02

innate immune response

8

3

2.2E-04

4.4E-02

Euclidian metric - Cluster 1g - Biological Process

Genes

% input

P-Value

Benjam

acute inflammatory response

8

3.8

1.5E-05

7.5E-02

humoral immune response by immunoglobulin

6

2.8

2.1E-05

5.3E-02

response to external stimulus

17

8.1

2.7E-05

4.6E-02

Euclidian metric - Cluster 1f - Biological Process

response to wounding

16

24.6

3.4E-14

1.7E-10

response to external stimulus

17

26.2

1.4E-12

3.6E-09

acute inflammatory response

9

13.8

1.8E-10

3.1E-07

acute-phase response

7

10.8

2.2E-10

2.9E-07

response to stress

17

26.2

3.4E-09

3.5E-06

wound healing

8

12.3

1.6E-08

1.4E-05

inflammatory response

10

15.4

3.6E-08

2.7E-05

blood coagulation

6

9.2

1.3E-06

8.5E-04

coagulation

6

9.2

1.4E-06

8.2E-04

hemostasis

6

9.2

1.7E-06

8.7E-04

regulation of body fluid levels

6

9.2

5.2E-06

2.4E-03

defense response

11

16.9

8.4E-05

3.6E-02


Genes heading indicates number of genes mapped to an ontology category. % input indicates the percentage of mapped genes from the total number of genes in the cluster. P-Value derived from Fishers exact test and Benjam indicates P-value after application of Benjamini multiple test correction.

Ryan et al. BMC Neuroscience 2010 11:107   doi:10.1186/1471-2202-11-107

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