PathDIP


37994706	PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. [PMID: 37994706] Chiara Pastrello, Max Kotlyar, Mark Abovsky, Richard Lu, Igor Jurisica Abstract Pathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all sources, separate sources or by combining specific pathway subsets; they can select the types of sources to use or the types of pathways for the analysis, reducing the number of resulting generic pathways or pathways not related to users' research question; users can use API. All pathways have been mapped to seven representative types. The results of pathway enrichment can be summarized through knowledge-based pathway consolidation. All curated pathways were mapped to 53 pathway ontology-based categories. In addition to genes, pathDIP 5 now includes metabolites. We updated existing databases, included two new sources, PathBank and MetabolicAtlas, and removed outdated databases. We enable users to analyse their results using Drugst.One, where a drug-gene network is created using only the user's genes in a specific pathway. Interpreting the results of any analysis is now improved by multiple charts on all the results pages. PathDIP 5 is freely available at https://ophid.utoronto.ca/pathDIP. Nucleic Acids Res. 2024:52(D1) \| 2 Citations (from Europe PMC, 2025-03-22)
31733064	pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. [PMID: 31733064] Rahmati S, Abovsky M, Pastrello C, Kotlyar M, Lu R, Cumbaa CA, Rahman P, Chandran V, Jurisica I. Abstract PathDIP was introduced to increase proteome coverage of literature-curated human pathway databases. PathDIP 4 now integrates 24 major databases. To further reduce the number of proteins with no curated pathway annotation, pathDIP integrates pathways with physical protein-protein interactions (PPIs) to predict significant physical associations between proteins and curated pathways. For human, it provides pathway annotations for 5366 pathway orphans. Integrated pathway annotation now includes six model organisms and ten domesticated animals. A total of 6401 core and ortholog pathways have been curated from the literature or by annotating orthologs of human proteins in the literature-curated pathways. Extended pathways are the result of combining these pathways with protein-pathway associations that are predicted using organism-specific PPIs. Extended pathways expand proteome coverage from 81 088 to 120 621 proteins, making pathDIP 4 the largest publicly available pathway database for these organisms and providing a necessary platform for comprehensive pathway-enrichment analysis. PathDIP 4 users can customize their search and analysis by selecting organism, identifier and subset of pathways. Enrichment results and detailed annotations for input list can be obtained in different formats and views. To support automated bioinformatics workflows, Java, R and Python APIs are available for batch pathway annotation and enrichment analysis. PathDIP 4 is publicly available at http://ophid.utoronto.ca/pathDIP. Nucleic Acids Res. 2020:48(D1) \| 32 Citations (from Europe PMC, 2025-03-22)
27899558	pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. [PMID: 27899558] Rahmati S, Abovsky M, Pastrello C, Jurisica I. Abstract Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5732 pathway orphans. PathDIP (http://ophid.utoronto.ca/pathdip) annotates 17 070 protein-coding genes with 4678 pathways, and provides multiple query, analysis and output options. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2017:45(D1) \| 58 Citations (from Europe PMC, 2025-03-22)

PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. [PMID: 37994706]

Chiara Pastrello, Max Kotlyar, Mark Abovsky, Richard Lu, Igor Jurisica

Pathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all sources, separate sources or by combining specific pathway subsets; they can select the types of sources to use or the types of pathways for the analysis, reducing the number of resulting generic pathways or pathways not related to users' research question; users can use API. All pathways have been mapped to seven representative types. The results of pathway enrichment can be summarized through knowledge-based pathway consolidation. All curated pathways were mapped to 53 pathway ontology-based categories. In addition to genes, pathDIP 5 now includes metabolites. We updated existing databases, included two new sources, PathBank and MetabolicAtlas, and removed outdated databases. We enable users to analyse their results using Drugst.One, where a drug-gene network is created using only the user's genes in a specific pathway. Interpreting the results of any analysis is now improved by multiple charts on all the results pages. PathDIP 5 is freely available at https://ophid.utoronto.ca/pathDIP.

Nucleic Acids Res. 2024:52(D1) | 2 Citations (from Europe PMC, 2025-03-22)

pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species. [PMID: 31733064]

Rahmati S, Abovsky M, Pastrello C, Kotlyar M, Lu R, Cumbaa CA, Rahman P, Chandran V, Jurisica I.

Abstract

PathDIP was introduced to increase proteome coverage of literature-curated human pathway databases. PathDIP 4 now integrates 24 major databases. To further reduce the number of proteins with no curated pathway annotation, pathDIP integrates pathways with physical protein-protein interactions (PPIs) to predict significant physical associations between proteins and curated pathways. For human, it provides pathway annotations for 5366 pathway orphans. Integrated pathway annotation now includes six model organisms and ten domesticated animals. A total of 6401 core and ortholog pathways have been curated from the literature or by annotating orthologs of human proteins in the literature-curated pathways. Extended pathways are the result of combining these pathways with protein-pathway associations that are predicted using organism-specific PPIs. Extended pathways expand proteome coverage from 81 088 to 120 621 proteins, making pathDIP 4 the largest publicly available pathway database for these organisms and providing a necessary platform for comprehensive pathway-enrichment analysis. PathDIP 4 users can customize their search and analysis by selecting organism, identifier and subset of pathways. Enrichment results and detailed annotations for input list can be obtained in different formats and views. To support automated bioinformatics workflows, Java, R and Python APIs are available for batch pathway annotation and enrichment analysis. PathDIP 4 is publicly available at http://ophid.utoronto.ca/pathDIP.

Nucleic Acids Res. 2020:48(D1) | 32 Citations (from Europe PMC, 2025-03-22)

pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. [PMID: 27899558]

Rahmati S, Abovsky M, Pastrello C, Jurisica I.

Abstract

Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding genes without any pathway annotations, i.e. 'pathway orphans'. In order to address all these challenges, we developed pathDIP, which integrates data from 20 source pathway databases, 'core pathways', with physical protein-protein interactions to predict biologically relevant protein-pathway associations, referred to as 'extended pathways'. Cross-validation determined 71% recovery rate of our predictions. Data integration and predictions increase coverage of pathway annotations for protein-coding genes to 86%, and provide novel annotations for 5732 pathway orphans. PathDIP (http://ophid.utoronto.ca/pathdip) annotates 17 070 protein-coding genes with 4678 pathways, and provides multiple query, analysis and output options. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2017:45(D1) | 58 Citations (from Europe PMC, 2025-03-22)

URL:	http://ophid.utoronto.ca/pathDIP
Full name:	Pathway Data Integration Portal
Description:	pathDIP 5 is an annotated database of signalling cascades in human and 16 non-human organisms, comprising 6,535 pathways, and covering 195148 genes and 5783 metabolites.pathDIP 5 substantially improves its integration into complex bioinformatics workflows, with programmatic and web-based enrichment analysis, knowledge-based pathway consolidation, integration with external tools such as Drugst.One, and implementation of multiple charts and heatmaps.
Year founded:	2017
Last update:	2024-02-13
Version:	v5.0.31.0
Accessibility:	Accessible
Country/Region:	Canada

Data type:	Protein RNA
Data object:	Animal Fungi
Database category:	Gene genome and annotation Interaction Literature Pathway Standard ontology and nomenclature
Major species:	Homo sapiens Saccharomyces cerevisiae Mus musculus Sus scrofa Gallus gallus Bos taurus Felis catus Canis familiaris Anas platyrhynchos Drosophila melanogaster Cavia porcellus Equus caballus Oryctolagus cuniculus Rattus norvegicus Ovis aries Meleagris gallopavo Lumbricus terrestris
Keywords:	enrichment analysis pathway annotation protein-protein interaction

University/Institution:	Schroeder Arthritis Institute
Address:	ON M5T 0S8, Canada
City:	Toronto
Province/State:
Country/Region:	Canada
Contact name (PI/Team):	Igor Jurisica
Contact email (PI/Helpdesk):	juris@ai.utoronto.ca

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Database Commons a catalog of worldwide biological databases