Although pathways are widely used for the analysis and representation of biological systems, their lack of clear boundaries, their dispersion across numerous databases, and the lack of interoperability impedes the evaluation of the coverage, agreements, and discrepancies between them. Here, we present ComPath, an ecosystem that supports curation of pathway mappings between databases and fosters the exploration of pathway knowledge through several novel visualizations. We have curated mappings between three of the major pathway databases and present a case study focusing on Parkinson's disease that illustrates how ComPath can generate new biological insights by identifying pathway modules, clusters, and cross-talks with these mappings. The ComPath source code and resources are available at https://github.com/ComPath and the web application can be accessed at https://compath.scai.fraunhofer.de/.
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists
Apoptosis in Alzheimer's disease: an understanding of the physiology, pathology and therapeutic avenues
Regulation of ATP13A2 via PHD2-HIF1α Signaling Is Critical for Cellular Iron Homeostasis: Implications for Parkinson's Disease
Towards a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment
Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data
Identification of Shared Molecular Signatures Indicate the Susceptibility of Endometriosis to Multiple Sclerosis
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations.
A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving.
Bioinformatics in Biomedicine
Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.