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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
WP2328: Allograft rejection
WP1041: Statin Pathway
WP673: ErbB signaling pathway
WP1144: B Cell Receptor Signaling Pathway
WP803: p38 MAPK Signaling Pathway (BioCarta)
WP127: IL-5 signaling pathway
WP911: Pentose Phosphate Pathway
WP1367: TGF-beta Receptor Signaling Pathway
WP3: Keap1-Nrf2 Pathway
WP1822: Generic Transcription Pathway
WP417: Oxidative Branch of the Pentose Phosphate Pathway
WP2199: Seed Development
WP10: IL-9 Signaling Pathway
WP557: ACE Inhibitor Pathway
WP1094: IL-6 Signaling Pathway
WP764: Hypothetical Network for Drug Addiction
WP1179: G13 Signaling Pathway
WP859: Complement Activation, Classical Pathway
WP1333: Hypothetical Network for Drug Addiction
WP946: Delta-Notch Signaling Pathway
WP2428: the quecetin and apoptosis pathway
WP1493: Carbon assimilation C4 pathway
WP372: Beta Oxidation Meta Pathway
WP2075: Alzheimers Disease
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 Topological integration of RPPA proteomic data with multi-omics data for survival prediction in breast cancer via pathway activity inference.
 Bioinformatics Analysis of the Core Genes Related to Lupus Nephritis Through a Network and Pathway-Based Approach.
 Network and pathway-based analysis of microRNA role in neuropathic pain in rat models.
 Pathway-based network analyses and candidate genes associated with Kashin-Beck disease.
 Investigation of multi-trait associations using pathway-based analysis of GWAS summary statistics.
 Pathway networks generated from human disease phenome.
 Analyzing the disease module associated with osteosarcoma via a network- and pathway-based approach.
 Pathway-based gene-gene interaction network modelling to predict potential biomarkers of essential hypertension.
 Human pathway-based disease network.
 Precision pharmacology for Alzheimer's disease.
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