ArticleBMC bioinformatics2017
dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- dictyBase 2026: a reimplementation of theResearch square · 2026Article
- IqgD is a Rac1-interacting IQGAP required for efficient growth of Dictyostelium discoideum on bacterial lawns.Cell communication and signaling : CCS · 2026Article
- Membrane microdomains are crucial forScience advances · 2026Article
- Related Dictyostelium G protein subunits Gα1 and Gα2 have different roles in chemotaxis and transcription factor regulation.BMC molecular and cell biology · 2025Article
- Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cell biology of Dictyostelium.BMC molecular and cell biology · 2025Article
- Mutual suppression between mutations in the Dictyostelium Greenbeard pathway restores wild-type development.BMC genomics · 2025Article
- Nuclear Envelope Dynamics inCells · 2025Review
- Copine C plays a role in adhesion and streaming inCell adhesion & migration · 2024Article
- Article
- Polycystin-2 Mediated Calcium Signalling in theCells · 2024Article
- Assaying Lysosomal Enzyme Activity in Dictyostelium discoideum.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Single Cell Transcriptome Analysis During Development in Dictyostelium.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Functional Prokaryotic-Like Deoxycytidine Triphosphate Deaminases and Thymidylate Synthase in Eukaryotic Social Amoebae: Vertical, Endosymbiotic, or Horizontal Gene Transfer?Molecular biology and evolution · 2023Article
- Lamins as structural nuclear elements through evolution.Current opinion in cell biology · 2023Review
- Article
- Yellow polyketide pigment suppresses premature hatching in social amoeba.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Dual regulation of the actin cytoskeleton by CARMIL-GAP.Journal of cell science · 2022Article
- Generation of a mitochondrial protein compendium iniScience · 2022Article
- An altered transcriptome underliesFrontiers in genetics · 2022Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundDictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomics and transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights.
resultsWe present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq). The application features visualization modules that include time course expression profiles, clustering, gene ontology enrichment analysis, differential expression analysis and comparison of experiments. All visualizations are interactive and interconnected, such that the selection of genes in one module propagates instantly to visualizations in other modules. dictyExpress currently stores the data from over 800 Dictyostelium experiments and is embedded within a general-purpose software framework for management of next-generation sequencing data. dictyExpress allows users to explore their data in a broader context by reciprocal linking with dictyBase-a repository of Dictyostelium genomic data. In addition, we introduce a companion application called GenBoard, an intuitive graphic user interface for data management and bioinformatics analysis.
conclusionsdictyExpress and GenBoard enable broad adoption of next generation sequencing based inquiries by the Dictyostelium research community. Labs without the means to undertake deep sequencing projects can mine the data available to the public. The entire information flow, from raw sequence data to hypothesis testing, can be accomplished in an efficient workspace. The software framework is generalizable and represents a useful approach for any research community. To encourage more wide usage, the backend is open-source, available for extension and further development by bioinformaticians and data scientists.
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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.