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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 [3537]
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.