ArticlePLoS computational biology2015
PathVisio 3: an extendable pathway analysis toolbox.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 247 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
247 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes.Genes to cells : devoted to molecular & cellular mechanisms · 2024Pooled it
- Genomic alterations in high-risk chronic lymphocytic leukemia frequently affect cell cycle key regulators and NOTCH1-regulated transcription.Haematologica · 2020Trial
- Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation.Scientific reports · 2020Trial
- Colonoid-Based Transcriptomics Reveals Conserved and Model-Specific Mechanisms of Doxorubicin-Induced Intestinal Toxicity.International journal of molecular sciences · 2026Article
- Deciphering Site-Specific Regulatory Networks of the Kinesin Protein KIF21A Through Integrative Phosphoproteomic Analysis.International journal of molecular sciences · 2026Article
- Metabolic pathway signatures define prognostic subtypes of lung adenocarcinoma.Discover oncology · 2026Article
- FAIR in practice: minimum metadata schema for bioinformatics analytics by machines.Journal of biomedical semantics · 2026Article
- Decoding the Oxylipin Chemical Space Using Ion Identity Molecular Networking.Analytical chemistry · 2026Article
- A dataset of rare copy number variants associated with neurodevelopmental and neuropsychiatric disorders.Scientific data · 2026Article
- Computational proteomics to enhance personalized treatment of COVID-19 and Long COVID.Clinical proteomics · 2026Review
- Pangenome Analysis and Genome-Guided Probiotic Evaluation of Cyclic Dipeptides Producing Levilactobacillus brevis DY55bre Strain from a Lactic Acid Fermented Shalgam to Assess Its Metabolic, Probiotic Potentials, and Cytotoxic Effects on Colorectal Cancer Cells.Probiotics and antimicrobial proteins · 2026Article
- Phosphorylation-dependent regulation of Eleven Lysine Rich Leukemia (ELL) uncovered by quantitative global phosphoproteomic analysis.Molecular genetics and genomics : MGG · 2026Article
- Specific SLC25 carriers regulate mitochondrial protein synthesis.Science advances · 2026Article
- Dissecting the Phospho-Regulatory Landscape of Protein Kinase N1 (PKN1) and Its Downstream Signaling: Functional Insights into the Activity-Dependent and Disease-Relevant Phosphosites.International journal of molecular sciences · 2026Article
- Phosphoproteome landscape of ARID1A and its implications in DNA damage response and breast cancer pathogenesis.Discover oncology · 2026Article
- ZMYM3 S464: a potential phospho-regulatory hub in epigenetic remodeling and oncogenesis.Molecular genetics and genomics : MGG · 2026Article
- Functional phosphoproteomic analysis of SMG1 in nonsense-mediated mRNA decay and DNA damage repair in cancer.Frontiers in systems biology · 2026Article
- Revealing RELL1 signaling relying on the phosphoregulatory network analysis.Frontiers in bioinformatics · 2026Article
- Unravelling the Phosphorylation Landscape of Anthrax Toxin Receptor 1: Mechanisms and Functional Insights Through Phosphoproteomic Data Integration.The protein journal · 2025Article
- Integration of elemental imaging and spatial transcriptomic profiling for proof-of-concept metals-based pathway analysis of colon tumor microenvironment.Metallomics : integrated biometal science · 2025Article
187 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.
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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.