ArticleBriefings in bioinformatics2022
Systematic assessment of pathway databases, based on a diverse collection of user-submitted experiments.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Causal network analysis of omics data using prior knowledge databases.Briefings in bioinformatics · 2025Pooled it
- Integrative Bioinformatics Identification of Baicalein as a Phytochemical Inhibitor of CHEK1 in Serous Ovarian Cancer: A Multi-Stage In Silico Drug Discovery Approach.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Review
- AI and network biology for rational polypharmacology in signaling drug design: a review.NPJ precision oncology · 2026Review
- A practical guide to functional enrichment analysis.Frontiers in bioinformatics · 2026Article
- Deciphering the Multi-Target Therapeutic Mechanisms of Traditional Chinese Medicine Against Alzheimer's Disease: A Network Pharmacology Perspective.Drug design, development and therapy · 2026Review
- Rethinking Alzheimer's: Harnessing Cannabidiol to Modulate IDO and cGAS Pathways for Neuroinflammation Control.eNeuro · 2025Article
- Patient-Specific Regulatory Network Rewiring in Inflammatory Bowel Disease: How Genetic Polymorphisms Divert Incoming Signals and Contribute to Disease Pathogenesis.Inflammatory bowel diseases · 2025Article
- Repurposing Cofilin-Targeting Compounds for Ischemic Stroke Through Cheminformatics and Network Pharmacology.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025Review
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- A workflow for human health hazard evaluation using transcriptomic data and Key Characteristics-based gene sets.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Mapping growth differentiation factor-15 (GDF15)-mediated signaling pathways in cancer: insights into its role across different cancer types.Discover oncology · 2025Article
- Article
- Spectral divergence prioritizes key classes, genes, and pathways shared between substance use disorders and cardiovascular disease.Frontiers in neuroscience · 2025Article
- Exploring Synaptic Pathways in Traumatic Brain Injury: A Cross-Phenotype Genomics Approach.Journal of neurotrauma · 2025Article
- Benchmarking enrichment analysis methods with the disease pathway network.Briefings in bioinformatics · 2024Article
- In Silico Models to Validate Novel Blood-Based Biomarkers.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A knowledge-based grouping of genes into pathways or functional units is essential for describing and understanding cellular complexity. However, it is not always clear a priori how and at what level of specificity functionally interconnected genes should be partitioned into pathways, for a given application. Here, we assess and compare nine existing and two conceptually novel functional classification systems, with respect to their discovery power and generality in gene set enrichment testing. We base our assessment on a collection of nearly 2000 functional genomics datasets provided by users of the STRING database. With these real-life and diverse queries, we assess which systems typically provide the most specific and complete enrichment results. We find many structural and performance differences between classification systems. Overall, the well-established, hierarchically organized pathway annotation systems yield the best enrichment performance, despite covering substantial parts of the human genome in general terms only. On the other hand, the more recent unsupervised annotation systems perform strongest in understudied areas and organisms, and in detecting more specific pathways, albeit with less informative labels.
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