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Constructing disease-disease similarity network is important in elucidating the associations between the origin and molecular mechanism of diseases, and in researching disease function and medical research. In this paper, we use a high-quality protein interaction network and a collection of pathway databases to construct a Human Pathway-based Disease Network (HPDN) to explore the relationship between diseases and their intrinsic interactions. We find that the similarity of two diseases has a strong correlation with the number of their shared functional pathways and the interaction between their related gene sets. Comparing HPDN with disease networks based on genes and symptoms respectively, we find the three networks have high overlap rates. Additionally, HPDN can predict new disease-disease correlations, which are supported by Comparative Toxicogenomics Database (CTD) benchmark and large-scale biomedical literature database. The comprehensive, high-quality relations between diseases based on pathways can further be applied to study important matters in systems medicine, for instance, drug repurposing. Based on a dense subgraph in our network, we find two drugs, prednisone and folic acid, may have new indications, which will provide potential directions for the treatments of complex diseases.
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WP2371: Parkinsons Disease Pathway
WP1: Statin Pathway
WP10: IL-9 Signaling Pathway
WP1004: Kit Receptor Signaling Pathway
WP1010: Wnt Signaling Pathway and Pluripotency
WP1011: T Cell Receptor Signaling Pathway
WP1012: IL-7 Signaling Pathway
WP1014: Androgen receptor signaling pathway
WP1016: Wnt Signaling Pathway
WP1019: FAS pathway and Stress induction of HSP regulation
WP1022: Hedgehog Signaling Pathway
WP1025: B Cell Receptor Signaling Pathway
WP1028: Pentose Phosphate Pathway
WP1029: Notch Signaling Pathway
WP1031: IL-3 Signaling Pathway
WP1033: ACE Inhibitor Pathway
WP1037: p38 MAPK Signaling Pathway
WP1040: Inflammatory Response Pathway
WP1041: Statin Pathway
WP1044: ErbB signaling pathway
WP1045: TGF-beta Receptor Signaling Pathway
WP1047: TNF-alpha NF-kB Signaling Pathway
WP1048: TGF Beta Signaling Pathway
WP1052: Id Signaling Pathway
WP1054: Polyol pathway
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 De novo pathway-based biomarker identification.
 Inherited variation in circadian rhythm genes and risks of prostate cancer and three other cancer sites in combined cancer consortia.
 A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease.
 Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach.
 The genetic basis for variation in resistance to infection in the Drosophila melanogaster genetic reference panel.
 The “Picardie en Forme” Network: Federating Regional Health-enhancing Sports Resources
 Pathway-analysis of published genome-wide association studies of lung cancer: A potential role for the CYP4F3 locus.
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