dictyExpress: an integrated browser for bulk and single-cell Dictyostelium transcriptomics

Abstract

Summary dictyExpress 3.0 is a React/TypeScript reimplementation of the Dictyostelium discoideum transcriptomics web server, first introduced in 2009, that unifies bulk and single-cell exploration. A long-standing gene-expression resource for the Dictyostelium community, dictyExpress is also accessible through dictyBase, the central organism database for Dictyostelium. The new release preserves the curated bulk RNA-seq dashboards of earlier versions while adding an interactive module for a developmental scRNA-seq time course of wild-type AX4 and two cAMP-signalling mutants. Following visual analytics principles, interactive visualizations are coordinated through brushing and linking, with bulk time courses, differential expression, gene-ontology enrichment and the UMAP workspace sharing a common gene selection, enabling bookmarkable and exportable cross-modal analysis in one interface for Dictyostelium transcriptomics. Availability and implementation dictyExpress is available at https://app.dictyexpress.org/. Source code: https://github.com/biolab/dictyexpress-js. Contact lena.trnovec@fri-uni-lj.si, blaz.zupan@fri.uni-lj.si