Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin...

Area of Science:

• Neuroscience
• Genomics
• Bioinformatics

Background:

• Gene expression and enhancer usage dynamics are crucial for understanding central nervous system (CNS) axon regeneration.
• Zebrafish models offer valuable insights into these complex regulatory mechanisms.

Purpose of the Study:

• To develop an interactive web application, Regeneration Rosetta, for exploring and functionally interpreting temporal transcription network data associated with regeneration.
• To enable researchers to investigate time-dependent gene regulation without requiring extensive bioinformatics expertise.

Main Methods:

• Development of an interactive web application, Regeneration Rosetta.
• Integration of time-course gene expression and enhancer usage data from zebrafish CNS axon regeneration studies.
• Implementation of features for gene list input (built-in or user-provided) across multiple organisms.

Main Results:

• Regeneration Rosetta facilitates visualization of clustered temporal expression trends.
• The application aids in identifying proximal and distal regions of accessible chromatin for motif analysis.
• It enables the description of enriched functional gene ontology categories.

Conclusions:

• Regeneration Rosetta provides a user-friendly platform for interrogating complex regeneration-associated temporal transcription data.
• The tool supports in-depth investigation of time-dependent gene regulation in zebrafish and facilitates hypothesis generation in other species.