ArticleNucleic acids research2016
PathwAX: a web server for network crosstalk based pathway annotation.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- TNFRSF1B Signaling Blockade Protects Airway Epithelial Cells from Oxidative Stress.Antioxidants (Basel, Switzerland) · 2024Article
- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.Nature communications · 2022Article
- Dual Costimulatory and Coinhibitory Targeting with a Hybrid Fusion Protein as an Immunomodulatory Therapy in Lupus Nephritis Mice Models.International journal of molecular sciences · 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
- Nextcast: A software suite to analyse and model toxicogenomics data.Computational and structural biotechnology journal · 2022Article
- Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.Frontiers in genetics · 2022Article
- The gene silencing of IRF5 and BLYSS effectively modulates the outcome of experimental lupus nephritis.Molecular therapy. Nucleic acids · 2021Article
- Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data.Scientific reports · 2021Article
- Action detection using a neural network elucidates the genetics of mouse grooming behavior.eLife · 2021Article
- Dual and Opposite Costimulatory Targeting with a Novel Human Fusion Recombinant Protein Effectively Prevents Renal Warm Ischemia Reperfusion Injury and Allograft Rejection in Murine Models.International journal of molecular sciences · 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
- Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data.NPJ systems biology and applications · 2020Article
- Pathway-specific model estimation for improved pathway annotation by network crosstalk.Scientific reports · 2020Article
- Fusion transcript detection using spatial transcriptomics.BMC medical genomics · 2020Article
- Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019Review
- Differential Connectivity in Colorectal Cancer Gene Expression NetworkIranian biomedical journal · 2019Article
- EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.Nucleic acids research · 2018Article
- Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.Nature communications · 2018Article
Corrections and comments
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Pathway annotation of gene lists is often used to functionally analyse biomolecular data such as gene expression in order to establish which processes are activated in a given experiment. Databases such as KEGG or GO represent collections of how genes are known to be organized in pathways, and the challenge is to compare a given gene list with the known pathways such that all true relations are identified. Most tools apply statistical measures to the gene overlap between the gene list and pathway. It is however problematic to avoid false negatives and false positives when only using the gene overlap. The pathwAX web server (http://pathwAX.sbc.su.se/) applies a different approach which is based on network crosstalk. It uses the comprehensive network FunCoup to analyse network crosstalk between a query gene list and KEGG pathways. PathwAX runs the BinoX algorithm, which employs Monte-Carlo sampling of randomized networks and estimates a binomial distribution, for estimating the statistical significance of the crosstalk. This results in substantially higher accuracy than gene overlap methods. The system was optimized for speed and allows interactive web usage. We illustrate the usage and output of pathwAX.
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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.