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Table 3 Contextual association of pathways

From: PathNet: a tool for pathway analysis using topological information

Frequency

Pathway name

(KEGG ID)

Overlap

References

   

(p-value)

 

5

Gap junction

(4540)

0.00

[50, 51]

5

GnRH signaling…

(4912)

0.00

[46, 47, 52]

5

Huntington’s…

(5016)

0.00

[30]

4

Adherens junction

(4520)

0.78

[26]

4

Axon guidance

(4360)

0.01

[31, 53]

4

Dorso-ventral

(4320)

0.24

NA

4

Insulin signaling

(4910)

0.03

[31]

4

Long-term depression

(4730)

0.00

[54, 55]

4

Long-term potentiation

(4720)

0.00

[31, 32]

4

Neurotrophin signal…

(4722)

0.01

[31, 48]

4

Oocyte meiosis

(4114)

0.00

NA

4

Pathways in cancer

(5200)

0.71

[35–37]

4

Ubiquitin media…

(4120)

1.00

[56, 57]

  1. Pathways that were contextually associated [p < 0.05 calculated from Eq. (6)] with the AD pathway from six comparisons (moderate and severe samples in the disease progression dataset; and primary visual cortex, hippocampal field CA1, middle temporal gyrus, and posterior cingulate cortex regions in the brain regions dataset). For comparison purpose, the fourth column shows the p-value of overlapping genes of a pathway and the AD pathway based on hypergeometric test. The ‘References’ column in the table provides support for the association each of the pathways to AD. NA: not available.