ArticleNucleic acids research2017
A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- A practical guide to functional enrichment analysis.Frontiers in bioinformatics · 2026Article
- Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.Journal of advanced research · 2025Review
- Computational Drug Repositioning in Cardiorenal Disease: Opportunities, Challenges, and Approaches.Proteomics · 2025Article
- PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation.Briefings in bioinformatics · 2024Article
- Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data.Bioinformatics (Oxford, England) · 2024Article
- Benchmarking enrichment analysis methods with the disease pathway network.Briefings in bioinformatics · 2024Article
- A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference.Briefings in functional genomics · 2022Article
- Identifying cellular cancer mechanisms through pathway-driven data integration.Bioinformatics (Oxford, England) · 2022Article
- Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways.Life (Basel, Switzerland) · 2022Article
- Characterization and Validation of ceRNA-Mediated Pathway-Pathway Crosstalk Networks Across Eight Major Cardiovascular Diseases.Frontiers in cell and developmental biology · 2022Article
- Network Crosstalk as a Basis for Drug Repurposing.Frontiers in genetics · 2022Article
- Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.Frontiers in genetics · 2022Article
- A combined approach for single-cell mRNA and intracellular protein expression analysis.Communications biology · 2021Article
- Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data.Scientific reports · 2021Article
- DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life.International journal of molecular sciences · 2021Article
- PathBIX-a web server for network-based pathway annotation with adaptive null models.Bioinformatics advances · 2021Article
- Analysing the meta-interaction between pathways by gene set topological impact analysis.BMC genomics · 2020Article
- Pathway-specific model estimation for improved pathway annotation by network crosstalk.Scientific reports · 2020Article
- Genome-wide functional association networks: background, data & state-of-the-art resources.Briefings in bioinformatics · 2020Review
- Pathway crosstalk perturbation network modeling for identification of connectivity changes induced by diabetic neuropathy and pioglitazone.BMC systems biology · 2019Article
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4 authors.
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Abstract
Analyzing gene expression patterns is a mainstay to gain functional insights of biological systems. A plethora of tools exist to identify significant enrichment of pathways for a set of differentially expressed genes. Most tools analyze gene overlap between gene sets and are therefore severely hampered by the current state of pathway annotation, yet at the same time they run a high risk of false assignments. A way to improve both true positive and false positive rates (FPRs) is to use a functional association network and instead look for enrichment of network connections between gene sets. We present a new network crosstalk analysis method BinoX that determines the statistical significance of network link enrichment or depletion between gene sets, using the binomial distribution. This is a much more appropriate statistical model than previous methods have employed, and as a result BinoX yields substantially better true positive and FPRs than was possible before. A number of benchmarks were performed to assess the accuracy of BinoX and competing methods. We demonstrate examples of how BinoX finds many biologically meaningful pathway annotations for gene sets from cancer and other diseases, which are not found by other methods. BinoX is available at http://sonnhammer.org/BinoX.
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