ArticlePlant physiology2005
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.
Article in Plant physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
46 citing papers in PubMed.
- Sustainable software development in science - insights from 20 years of Vanted.Journal of integrative bioinformatics · 2025Article
- Harnessing multi-omics approaches to combat Karnal bunt of wheat: a review of advances and future prospects.Frontiers in genetics · 2025Review
- Wheat Omics: Advancements and Opportunities.Plants (Basel, Switzerland) · 2023Review
- A comprehensive survey of the approaches for pathway analysis using multi-omics data integration.Briefings in bioinformatics · 2022Review
- Understanding saffron biology using omics- and bioinformatics tools: stepping towards a better Crocus phenome.Molecular biology reports · 2022Article
- Co-Expression Network and Time-Course Expression Analyses to Identify Silk Protein Regulatory Factors inInsects · 2022Article
- CPA: a web-based platform for consensus pathway analysis and interactive visualization.Nucleic acids research · 2021Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Applications of Multi-Omics Technologies for Crop Improvement.Frontiers in plant science · 2021Review
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.Metabolites · 2019Article
- Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation.Scientific reports · 2018Article
- PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.Nucleic acids research · 2018Article
- Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Frontiers in plant science · 2018Review
- From correlation to causation: analysis of metabolomics data using systems biology approaches.Metabolomics : Official journal of the Metabolomic Society · 2018Review
- Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure.Plant physiology · 2016Article
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
- Precise sequential DNA ligation on a solid substrate: solid-based rapid sequential ligation of multiple DNA molecules.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- 3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.BMC systems biology · 2013Article
- Recent progress in the development of metabolome databases for plant systems biology.Frontiers in plant science · 2013Article
- Integrated LC-MS/MS system for plant metabolomics.Computational and structural biotechnology journal · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.
Indexed as
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.