ArticleBMC bioinformatics2016
Pathway collages: personalized multi-pathway diagrams.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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.
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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
15 citing papers in PubMed.
- Neoantigenic receptor ROR1 promotes cell growth through diverse and complementary mechanisms.Leukemia · 2026Article
- Metaproteomics uncovers the functional capacity of a soil microbiome.Scientific reports · 2026Article
- Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126.PloS one · 2025Article
- The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data.Metabolites · 2024Article
- Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19.Life science alliance · 2021Article
- Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook.Briefings in bioinformatics · 2021Article
- The BioCyc Metabolic Network Explorer.BMC bioinformatics · 2021Article
- Pathway Tools Visualization of Organism-Scale Metabolic Networks.Metabolites · 2021Article
- Repurposing the orphan drug nitisinone to control the transmission of African trypanosomiasis.PLoS biology · 2021Article
- Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus.Biotechnology for biofuels · 2020Article
- Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs.Scientific reports · 2019Article
- Using Pathway Covering to Explore Connections among Metabolites.Metabolites · 2019Article
- Navigating the disease landscape: knowledge representations for contextualizing molecular signatures.Briefings in bioinformatics · 2019Review
- Integrating bioinformatics approaches for a comprehensive interpretation of metabolomics datasets.Current opinion in biotechnology · 2018Review
- The Omics Dashboard for interactive exploration of gene-expression data.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
backgroundMetabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions?
resultsWe define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and an Escherichia coli metabolic model.
conclusionsPathway collages enable facile construction of personalized multi-pathway diagrams.
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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.