ArticleBMC bioinformatics2009
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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
42 citing papers in PubMed.
- dictyBase 2026: a reimplementation of theResearch square · 2026Article
- Mfsd8 Modulates Growth and the Early Stages of Multicellular Development inFrontiers in cell and developmental biology · 2022Article
- Changes of the tRNA Modification Pattern during the Development ofNon-coding RNA · 2021Article
- Inhibiting Neddylation with MLN4924 Suppresses Growth and Delays Multicellular Development inBiomolecules · 2021Article
- Review
- Unusual Occurrence of Two Bona-Fide CCA-Adding Enzymes inInternational journal of molecular sciences · 2020Article
- Cytokinins in Dictyostelia - A Unique Model for Studying the Functions of Signaling Agents From Species to Kingdoms.Frontiers in cell and developmental biology · 2020Review
- Cytokinin Detection during theBiomolecules · 2019Article
- Article
- Review
- Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae.Scientific reports · 2018Article
- The cAMP-induced G protein subunits dissociation monitored in live Dictyostelium cells by BRET reveals two activation rates, a positive effect of caffeine and potential role of microtubules.Cellular signalling · 2018Article
- CBP7 Interferes with the Multicellular Development ofMolecules and cells · 2018Article
- Aberrant adhesion impacts early development in a Dictyostelium model for juvenile neuronal ceroid lipofuscinosis.Cell adhesion & migration · 2017Article
- dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.BMC bioinformatics · 2017Article
- Protein kinase A regulates the Ras, Rap1 and TORC2 pathways in response to the chemoattractant cAMP inJournal of cell science · 2017Article
- The Long Noncoding RNA Transcriptome ofG3 (Bethesda, Md.) · 2017Article
- Improved annotation with de novo transcriptome assembly in four social amoeba species.BMC genomics · 2017Article
- Using the social amoeba Dictyostelium to study the functions of proteins linked to neuronal ceroid lipofuscinosis.Journal of biomedical science · 2016Review
- Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundBioinformatics often leverages on recent advancements in computer science to support biologists in their scientific discovery process. Such efforts include the development of easy-to-use web interfaces to biomedical databases. Recent advancements in interactive web technologies require us to rethink the standard submit-and-wait paradigm, and craft bioinformatics web applications that share analytical and interactive power with their desktop relatives, while retaining simplicity and availability.
resultsWe have developed dictyExpress, a web application that features a graphical, highly interactive explorative interface to our database that consists of more than 1000 Dictyostelium discoideum gene expression experiments. In dictyExpress, the user can select experiments and genes, perform gene clustering, view gene expression profiles across time, view gene co-expression networks, perform analyses of Gene Ontology term enrichment, and simultaneously display expression profiles for a selected gene in various experiments. Most importantly, these tasks are achieved through web applications whose components are seamlessly interlinked and immediately respond to events triggered by the user, thus providing a powerful explorative data analysis environment.
conclusiondictyExpress is a precursor for a new generation of web-based bioinformatics applications with simple but powerful interactive interfaces that resemble that of the modern desktop. While dictyExpress serves mainly the Dictyostelium research community, it is relatively easy to adapt it to other datasets. We propose that the design ideas behind dictyExpress will influence the development of similar applications for other model organisms.
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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.