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Table 1 Enrichment of pathways associated with AD

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

Pathway (KEGG ID) PathNet SPIA GSEA Hypergeometric test
Inc Mod Sev HIP Inc Mod Sev HIP Inc Mod Sev HIP Inc Mod Sev HIP
AD pathway (5010) 1.00 *0.01 *0.00 *0.00 1.00 0.14 *0.00 *0.01 1.00 0.81 0.72 0.34 1.00 0.06 *0.00 *0.00
Focal adhesion (4510) 1.00 *0.00 *0.00 *0.00 1.00 1.00 1.00 0.28 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
Long-term pote… (4720) 1.00 *0.00 *0.01 *0.04 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.37 1.00 1.00 1.00 1.00
Regulation of a… (4810) *0.00 *0.00 *0.00 *0.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
Phosphatidylino… (4070) 1.00 0.11 *0.00 0.52      1.00 1.00 0.54 1.00 1.00 1.00 0.21 1.00
Wnt signaling (4310) *0.00 1.00 *0.00 *0.03 1.00 1.00 0.92 1.00 1.00 1.00 1.00 0.91 1.00 1.00 1.00 1.00
Adherens junct… (4520) 1.00 *0.00 0.13 *0.00      0.95 0.31 0.96 0.38 1.00 1.00 0.48 *0.01
Ubiquitin media… (4120) 1.00 1.00 1.00 0.13      1.00 1.00 1.00 0.92 1.00 1.00 1.00 0.17
  1. Enrichment (pFWER: family-wise error rate corrected p-values) of pathways associated with Alzheimer’s disease (AD) using four different pathway analysis methods (i.e., PathNet: the present study, SPIA: signaling pathway impact analysis, GSEA: gene set enrichment analysis, and the hypergeometric test), from the disease progression dataset (Inc: incipient, Mod: moderate, and Sev: severe) and from the brain regions dataset (HIP: hippocampal field CA1 region). The complete set of data is included in Additional files3, Additional files4, and Additional files5. The statistically significant p fwer - values (p fwer  < 0.05) for each pathway and method are indicated by an asterisk (*). PathNet was able to identify these pathways as significant more often than each of the other three methods. SPIA was not applicable (represented by missing enrichment scores) when certain topological characteristics of the pathway was not met.