|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.
|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|
|PubMed:||31575636 Full text @ G3 (Bethesda)|
Rau, A., Dhara, S.P., Udvadia, A.J., Auer, P.L. (2019) Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility. G3 (Bethesda). 9(12):3953-3959.
ABSTRACTTime-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.
- Genes / Markers (13)