ZFIN ID: ZDB-PUB-191003-3
Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility
Rau, A., Dhara, S.P., Udvadia, A.J., Auer, P.L.
Date: 2019
Source: G3 (Bethesda)   9(12): 3953-3959 (Journal)
Registered Authors: Udvadia, Ava J.
Keywords: CNS axon regeneration, R/Shiny, chromatin accessibility, functional enrichment, gene expression, zebrafish
MeSH Terms:
  • Animals
  • Biological Evolution
  • Cholesterol/metabolism
  • Chromatin/metabolism*
  • Gene Expression Regulation, Developmental*
  • Genome
  • Internet*
  • Lipids/biosynthesis
  • Nerve Regeneration/genetics*
  • Optic Nerve/pathology
  • Optic Nerve/physiopathology
  • Software*
  • Zebrafish/genetics
PubMed: 31575636 Full text @ G3 (Bethesda)
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ABSTRACT
Time-course high-throughput assays of gene expression and enhancer usage in zebrafish provide a valuable characterization of the dynamic mechanisms governing gene regulatory programs during CNS axon regeneration. To facilitate the exploration and functional interpretation of a set of fully-processed data on regeneration-associated temporal transcription networks, we have created an interactive web application called Regeneration Rosetta Using either built-in or user-provided lists of genes in one of dozens of supported organisms, our web application facilitates the (1) visualization of clustered temporal expression trends; (2) identification of proximal and distal regions of accessible chromatin to expedite downstream motif analysis; and (3) description of enriched functional gene ontology categories. By enabling a straightforward interrogation of these rich data without extensive bioinformatic expertise, Regeneration Rosetta is broadly useful for both a deep investigation of time-dependent regulation during regeneration in zebrafish and hypothesis generation in other organisms.
ADDITIONAL INFORMATION