PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources

Area of Science:

• Developmental Biology
• Genomics
• Systems Biology

Background:

• The increasing volume of transcriptomic and genomic data from planarian research presents challenges in analysis.
• Understanding planarian regeneration and development requires effective tools for data exploration and visualization.

Purpose of the Study:

• To introduce PlanExp, a web application designed for exploring and visualizing gene expression data in planarians.
• To facilitate the integration of diverse RNA sequencing (RNA-seq) data, including traditional and single-cell RNA-seq.

Main Methods:

• Development of a web application, PlanExp, for interactive data visualization.
• Integration with the PlanNET web application for linking expression data with sequence annotations.
• Implementation of a gene/protein network editor and a network expression mapper.

Main Results:

• PlanExp offers tools for creating interactive plots like heatmaps and scatterplots.
• The application links gene expression data with genome and transcript-level annotations.
• Features include genetic interaction prediction from single-cell RNA-seq and network expression mapping.

Conclusions:

• PlanExp provides a valuable resource for researchers studying planarian biology.
• The tool aims to bridge the gap between systems biology approaches and the study of planarian regeneration.