ArticleF1000Research2014
KEGGscape: a Cytoscape app for pathway data integration.
Article in F1000Research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
58 citing papers in PubMed.
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- Establishment of a chemoresistant laryngeal cancer cell model to study chemoresistance and chemosensitization responses via transcriptomic analysis and a tumor-on-a-chip platform.Bioengineering & translational medicine · 2025Article
- Phage reprogramming ofmBio · 2025Article
- PACO: a Shiny app for comparing perturbed pathways associated with different phenotypes.Bioinformatics advances · 2025Article
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- Tracking Metabolite Variations during the Degradation of Vegetables in Rice Bran Bed with Intact-State Nuclear Magnetic Resonance Spectroscopy.Metabolites · 2024Article
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- Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification.Frontiers in medical technology · 2024Review
- Naringin and temozolomide combination suppressed the growth of glioblastoma cells by promoting cell apoptosis: network pharmacology,Frontiers in pharmacology · 2024Article
- Epigenetic Profiles of Triple-Negative Breast Cancers of African American and White Females.JAMA network open · 2023Article
- Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations.Orphanet journal of rare diseases · 2023Article
- PSF toolkit: an R package for pathway curation and topology-aware analysis.Frontiers in genetics · 2023Article
- Protein-Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow.Life (Basel, Switzerland) · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.
Identifiers
What OpenQuestion holds
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.