URL: | https://pathcards.genecards.org/ |
Full name: | Human Biological Pathway Unification |
Description: | PathCards is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more human pathways. It includes 1,648 SuperPath entries, consolidated from 11 selected web sources and is modeled on the architecture and richness of the popular GeneCards database of human genes. |
Year founded: | 2014 |
Last update: | 2024-04-27 |
Version: | 5.21 |
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Country/Region: | Israel |
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University/Institution: | Weizmann Institute of Science |
Address: | Department of Molecular Genetics, Weizmann Institute of Science 234 Herzl St. Rehovot, 76100, Israel |
City: | Rehovot |
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Country/Region: | Israel |
Contact name (PI/Team): | Doron Lancet |
Contact email (PI/Helpdesk): | doron.lancet@weizmann.ac.il |
PathCards: multi-source consolidation of human biological pathways. [PMID: 25725062]
The study of biological pathways is key to a large number of systems analyses. However, many relevant tools consider a limited number of pathway sources, missing out on many genes and gene-to-gene connections. Simply pooling several pathways sources would result in redundancy and the lack of systematic pathway interrelations. To address this, we exercised a combination of hierarchical clustering and nearest neighbor graph representation, with judiciously selected cutoff values, thereby consolidating 3215 human pathways from 12 sources into a set of 1073 SuperPaths. Our unification algorithm finds a balance between reducing redundancy and optimizing the level of pathway-related informativeness for individual genes. We show a substantial enhancement of the SuperPaths' capacity to infer gene-to-gene relationships when compared with individual pathway sources, separately or taken together. Further, we demonstrate that the chosen 12 sources entail nearly exhaustive gene coverage. The computed SuperPaths are presented in a new online database, PathCards, showing each SuperPath, its constituent network of pathways, and its contained genes. This provides researchers with a rich, searchable systems analysis resource. Database URL: http://pathcards.genecards.org/ |