dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Dictyostelium discoideum serves as a model organism for studying diverse biological processes.
• Advancements in next-generation sequencing (NGS) have generated large datasets for genomics and transcriptomics.
• Analyzing high-dimensional NGS data presents challenges for hypothesis generation and insight discovery.

Purpose of the Study:

• To introduce dictyExpress (2.0), a web application for exploratory analysis of gene expression and ChIP-Seq data.
• To provide interactive visualization modules for time course expression, clustering, and differential expression analysis.
• To present GenBoard, a companion GUI for data management and bioinformatics analysis.

Main Methods:

• Development of dictyExpress (2.0) with interactive, interconnected visualization modules.
• Integration of over 800 Dictyostelium experiments and linkage with dictyBase.
• Creation of GenBoard for intuitive data management and bioinformatics workflows.

Main Results:

• dictyExpress (2.0) offers time course profiles, clustering, gene ontology enrichment, and differential expression analysis.
• Interactive visualizations allow seamless gene selection across modules.
• The system links to dictyBase for broader genomic data context.

Conclusions:

• dictyExpress and GenBoard empower the Dictyostelium research community to utilize NGS data effectively.
• Publicly available data can be mined by labs lacking extensive sequencing resources.
• The open-source framework supports efficient data analysis from raw sequences to hypothesis testing.