ArticleNucleic acids research2024
PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Integrating dorsolateral prefrontal cortex multi-omics and GWAS summary data reveals genetic etiology of Parkinson's disease.medRxiv : the preprint server for health sciences · 2026Article
- Cell-type-aware transcriptome-wide association studies identify 91 independent risk genes for Alzheimer's disease dementia.Communications biology · 2026Article
- IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks.Nucleic acids research · 2026Article
- Altered microRNA profiles and associated pathways in canine mammary adenocarcinoma.Scientific reports · 2025Article
- A proteomics investigation of primary human articular chondrocyte isolation.Osteoarthritis and cartilage open · 2025Article
- Bioinformatics analysis of Rickettsia typhi autoimmune associations and screening of Streptomyces-derived inhibitors.BioData mining · 2025Article
- Sex differences in serum proteomic profiles in psoriatic arthritis.Rheumatology (Oxford, England) · 2025Article
- A microRNA CRISPR screen reveals microRNA-483-3p as an apoptotic regulator in prostate cancer cells.Cell death & disease · 2025Article
- Changes in peripheral blood and cognitive performance after nonconcussive head impacts in elite female soccer players.Communications medicine · 2025Article
- From mechanism to medicine: The progress and potential of epigenetics in osteoarthritis.Osteoarthritis and cartilage open · 2025Review
- Ten practical tips and tricks to improve the effectiveness of biological network alignment.PLoS computational biology · 2025Article
- Circulating microRNA profiles in early-stage osteoarthritis and rheumatoid arthritis.Scientific reports · 2025Article
- Identification of miR-190a-5p and miR-26b-5p as Potential microRNA Biomarkers for Psoriatic Arthritis.ACR open rheumatology · 2025Article
- Distinct inflammatory profiles in young-onset versus late-onset Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- Network insights into childhood obesity: unveiling methylated-differentially expressed genes and pathways through integrative bioinformatics analysis.Endocrine connections · 2025Article
- Integrative immunology identified interferome signatures in uveitis and systemic disease-associated uveitis.Frontiers in immunology · 2025Article
- Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing.Nucleic acids research · 2024Article
- Molecular landscape of kidney allograft tissues data integration portal (NephroDIP): a curated database to improve integration of high-throughput kidney transplant datasets.Frontiers in immunology · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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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.