ArticleNucleic acids research2017
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Impact of lncRNAs in Diabetes Mellitus: A Systematic Review andFrontiers in endocrinology · 2021Pooled it
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- Elucidating the roles of microRNA-103a-3p in trophoblast invasion and SOX4-mediated extravillous differentiation induced by activin A.Cell death & disease · 2026Article
- Copy number variants and the tangential expansion of the cerebral cortex.Nature communications · 2025Article
- Bioinformatic challenges for pharmacogenomic study: tools for genomic data analysis.Frontiers in pharmacology · 2025Article
- ShinyDegSEM: an interactive application for pathway perturbation analysis in gene expression studiesPeerJ · 2025Article
- New insights into the molecular biology of Alzheimer's-like cerebral amyloidosis achieved through multi-omics approaches.PloS one · 2025Article
- Single-cell RNA sequencing of circulating immune cells supports inhibition ofFrontiers in immunology · 2025Article
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- Identification of metabolic pathways and key genes associated with atypical parkinsonism using a systems biology approach.Metabolic brain disease · 2024Article
- PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful.Nucleic acids research · 2024Article
- Differential gene expression analysis based on linear mixed model corrects false positive inflation for studying quantitative traits.Scientific reports · 2023Article
- Mining Autoimmune-Disorder-Linked Molecular-Mimicry Candidates inMicroorganisms · 2023Article
- Molecular Mimicry Mapping inPathogens (Basel, Switzerland) · 2023Article
- The miRNA Content of Bone Marrow-Derived Extracellular Vesicles Contributes to Protein Pathway Alterations Involved in Ionising Radiation-Induced Bystander Responses.International journal of molecular sciences · 2023Article
- Longitudinal multi-omics alterations response to 8-week risperidone monotherapy: Evidence linking cortical thickness, transcriptomics and epigenetics.Frontiers in psychiatry · 2023Article
- The lncRNA MALAT1 is upregulated in urine of type 1 diabetes mellitus patients with diabetic kidney disease.Genetics and molecular biology · 2023Article
- Identification of a differential metabolite-based signature in patients with late-stage knee osteoarthritis.Osteoarthritis and cartilage open · 2022Article
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4 authors.
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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.
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