dictyExpress
1.1.0An interactive, exploratory data analytics web-app that provides access to gene expression experiments in Dictyostelium by Baylor College of Medicine.
Features
Plot and explore RNA-seq gene expressions of D. discoideum and D. purpureum
Find clusters of expressed genes and play with Gene Ontology enrichment analysis
Compare gene expression across different strains and explore cell-type specific expressions
Interactive design with clickable plots where selections propagate to other modules
Screenshots
The Experiment and Gene selection module sets the experiment and a set of genes for the analysis.
Citing dictyExpress
Stajdohar M, Rosengarten RD, Kokosar J, Jeran L, Blenkus D, Shaulsky G, Zupan B. "dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond." BMC Bioinformatics. 2017. 18(1):291
References
Transcriptional milestones in Dictyostelium development
Katoh-Kurasawa M, Hrovatin K, Hirose S, Webb A, Ho H, Zupan B, Shaulsky G
Genome Research 2021
Swatson WS, Katoh-Kurasawa M, Shaulsky G, Alexander S
PLoS One 2017
The long noncoding RNA transcriptome of Dictyostelium discoideum development
Rosengarten RD, Santhanam B, Kokosar J, Shaulsky G
Genes|Genomes|Genetics (G3) 2017
The GATA transcription factor gene gtaG is required for terminal differentiation in Dictyostelium
Katoh-Kurasawa M, Santhanam B, Shaulsky G
Journal of Cell Science 2016
Terpene synthase genes in eukaryotes beyond
plants and fungi: Occurrence in social amoebae
Chen X, Köllner TG, Jia Q, Norris A, Santhanam B, Rabe P, Dickschat JS, Shaulsky G, Gershenzon J, Chen F
PNAS 2016
Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum
Rosengarten RD, Santhanam B, Fuller D, Katoh-Kurasawa M, Loomis WF, Zupan B, Shaulsky G
BMC Genomics 2015
Hirose S, Santhanam B, Katoh-Kurasawa M, Shaulsky G, Kuspa A
Development 2015
Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M
Nature Communications 2015
Conserved developmental transcriptomes
in evolutionary divergent species
Parikh A, Miranda ER, Katoh-Kurasawa M, Fuller D, Rot G, Zagar L, Curk T, Sucgang R, Chen R, Zupan B, Loomis WF, Kuspa A, Shaulsky G
Genome Biology 2010
Rot G, Parikh A, Curk T, Kuspa A, Shaulsky G, Zupan B
BMC Bioinformatics 2009
Credits
dictyExpress was built in collaboration with
Bioinformatics Laboratory at University of Ljubljana
Gad Shaulsky's and Adam Kuspa's labs at Baylor College of Medicine
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Get in touch
If you have an idea of how to improve dictyExpress
or to add extra functionality, please contact us.