ArticlePloS one2009
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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
34 citing papers in PubMed.
- UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets.Computational and structural biotechnology journal · 2022Article
- Insights into physiological roles of unique metabolites released from Plasmodium-infected RBCs and their potential as clinical biomarkers for malaria.Scientific reports · 2019Article
- iPath3.0: interactive pathways explorer v3.Nucleic acids research · 2018Article
- Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic OrganismFrontiers in microbiology · 2018Article
- Signalling maps in cancer research: construction and data analysis.Database : the journal of biological databases and curation · 2018Article
- Pathview Web: user friendly pathway visualization and data integration.Nucleic acids research · 2017Article
- NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.Database : the journal of biological databases and curation · 2017Article
- De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.BMC genomics · 2016Article
- Article
- Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.PLoS computational biology · 2015Article
- Wormpath: searching for molecular interaction networks in Caenorhabditis elegans.Source code for biology and medicine · 2015Article
- KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments.Computational and structural biotechnology journal · 2015Article
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
- Tools for visualization and analysis of molecular networks, pathways, and -omics data.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- Metabolic fingerprinting of Arabidopsis thaliana accessions.Frontiers in plant science · 2015Article
- Article
- Hsa-miR-195 targets PCMT1 in hepatocellular carcinoma that increases tumor life span.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Article
- KEGGscape: a Cytoscape app for pathway data integration.F1000Research · 2014Article
- Entourage: visualizing relationships between biological pathways using contextual subsets.IEEE transactions on visualization and computer graphics · 2013Article
- NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.BMC systems biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiochemical pathways provide an essential context for understanding comprehensive experimental data and the systematic workings of a cell. Therefore, the availability of online pathway browsers will facilitate post-genomic research, just as genome browsers have contributed to genomics. Many pathway maps have been provided online as part of public pathway databases. Most of these maps, however, function as the gateway interface to a specific database, and the comprehensiveness of their represented entities, data mapping capabilities, and user interfaces are not always sufficient for generic usage. METHODOLOGY/PRINCIPAL
findingsWe have identified five central requirements for a pathway browser: (1) availability of large integrated maps showing genes, enzymes, and metabolites; (2) comprehensive search features and data access; (3) data mapping for transcriptomic, proteomic, and metabolomic experiments, as well as the ability to edit and annotate pathway maps; (4) easy exchange of pathway data; and (5) intuitive user experience without the requirement for installation and regular maintenance. According to these requirements, we have evaluated existing pathway databases and tools and implemented a web-based pathway browser named Pathway Projector as a solution. CONCLUSIONS/SIGNIFICANCE: Pathway Projector provides integrated pathway maps that are based upon the KEGG Atlas, with the addition of nodes for genes and enzymes, and is implemented as a scalable, zoomable map utilizing the Google Maps API. Users can search pathway-related data using keywords, molecular weights, nucleotide sequences, and amino acid sequences, or as possible routes between compounds. In addition, experimental data from transcriptomic, proteomic, and metabolomic analyses can be readily mapped. Pathway Projector is freely available for academic users at (http://www.g-language.org/PathwayProjector/).
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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.