ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2007
Discovery of protein interaction networks shared by diseases.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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Who cites it
26 citing papers in PubMed, 56 citations in OpenAlex.
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- Convergent downstream candidate mechanisms of independent intergenic polymorphisms between co-classified diseases implicate epistasis among noncoding elements.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
- Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores.Frontiers in genetics · 2017Article
- Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records.Yearbook of medical informatics · 2016Review
- eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs.Journal of biomedical informatics · 2015Article
- A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.Systems and synthetic biology · 2014Article
- Protein-protein interaction networks (PPI) and complex diseases.Gastroenterology and hepatology from bed to bench · 2014Review
- Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes.BioMed research international · 2014Article
- Prediction of novel genes associated with negative regulators of toll-like receptors-induced inflammation based on endotoxin tolerance.Inflammation · 2012Article
- Data driven linear algebraic methods for analysis of molecular pathways: application to disease progression in shock/trauma.Journal of biomedical informatics · 2012Article
- A vertex similarity-based framework to discover and rank orphan disease-related genes.BMC systems biology · 2012Article
- Formal concept analysis of disease similarity.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2012Article
- Multi-dimensional discovery of biomarker and phenotype complexes.BMC bioinformatics · 2010Article
- Molecular mechanistic associations of human diseases.BMC systems biology · 2010Article
- A quantitative approach to study indirect effects among disease proteins in the human protein interaction network.BMC systems biology · 2010Article
- Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures.Journal of biomedical informatics · 2010Article
- The power of protein interaction networks for associating genes with diseases.Bioinformatics (Oxford, England) · 2010Article
- Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine.Summit on translational bioinformatics · 2010Article
- Advances in translational bioinformatics: computational approaches for the hunting of disease genes.Briefings in bioinformatics · 2010Article
- Network analysis of genes regulated in renal diseases: implications for a molecular-based classification.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The study of protein-protein interactions is essential to define the molecular networks that contribute to maintain homeostasis of an organism's body functions. Disruptions in protein interaction networks have been shown to result in diseases in both humans and animals. Monogenic diseases disrupting biochemical pathways such as hereditary coagulopathies (e.g. hemophilia), provided a deep insight in the biochemical pathways of acquired coagulopathies of complex diseases. Indeed, a variety of complex liver diseases can lead to decreased synthesis of the same set of coagulation factors as in hemophilia. Similarly, more complex diseases such as different cancers have been shown to result from malfunctions of common proteins pathways. In order to discover, in high throughput, the molecular underpinnings of poorly characterized diseases, we present a statistical method to identify shared protein interaction network(s) between diseases. Integrating (i) a protein interaction network with (ii) disease to protein relationships derived from mining Gene Ontology annotations and the biomedical literature with natural language understanding (PhenoGO), we identified protein-protein interactions that were associated with pairs of diseases and calculated the statistical significance of the occurrence of interactions in the protein interaction knowledgebase. Significant correlations between diseases and shared protein networks were identified and evaluated in this study, demonstrating the high precision of the approach and correct non-trivial predictions, signifying the potential for discovery. In conclusion, we demonstrate that the associations between diseases are directly correlated to their underlying protein-protein interaction networks, possibly providing insight into the underlying molecular mechanisms of phenotypes and biological processes disrupted in related diseases.
Indexed as
Identifiers
17992746PMC2886192W2075155461What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.