PlanExp

PlanExp provides exploration, visualization, and analysis of RNA-seq datasets from the planarian Schmidtea mediterranea to support studies of regeneration and development.

Key Features:

• Support for sequencing technologies: Integration of traditional bulk RNA-seq and single-cell RNA-seq datasets for combined transcriptomic analyses.
• Interactive visualization tools: Generation and manipulation of visualizations including heatmaps and scatterplots for examination of gene expression patterns.
• Integration with sequence annotations (PlanNET): Linking of gene expression data to sequence annotations at genome and transcript levels via PlanNET.
• Gene/protein network editor: Construction and analysis of gene and protein interaction networks for systems-level investigation.
• Prediction of genetic interactions: Derivation of predicted genetic interactions from single-cell RNA-seq data.
• Network expression mapper: Mapping of gene expression values onto biological networks to relate expression patterns to network contexts.

Scientific Applications:

• Planarian regeneration and development: Analysis of expression dynamics and regulatory interactions underlying regeneration and developmental processes in Schmidtea mediterranea.
• Gene expression studies: Comparative and exploratory analyses of gene- and transcript-level expression across RNA-seq experiments.
• Systems biology and network analysis: Network-based interpretation of transcriptomic data to identify pathways and interaction modules.
• Prediction and prioritization of genetic interactions: Identification of candidate genetic interactions for experimental validation using single-cell RNA-seq–derived predictions.

Methodology:

Integration of bulk and single-cell RNA-seq datasets with genomic and transcript annotations via PlanNET; generation of heatmaps and scatterplots; construction and analysis of gene/protein networks; mapping of expression onto networks; prediction of genetic interactions from single-cell RNA-seq data.