Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility. G3 (Bethesda) 2019 Dec 03;9(12):3953-3959
Date
10/03/2019Pubmed ID
31575636Pubmed Central ID
PMC6893199DOI
10.1534/g3.119.400729Scopus ID
2-s2.0-85076061492 (requires institutional sign-in at Scopus site) 3 CitationsAbstract
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.
Author List
Rau A, Dhara SP, Udvadia AJ, Auer PLAuthors
Paul L. Auer PhD Professor in the Data Science Institute department at Medical College of WisconsinAva Udvadia BS,PhD Associate Professor in the Biological Sciences department at University of Wisconsin - Milwaukee
MESH terms used to index this publication - Major topics in bold
AnimalsBiological Evolution
Cholesterol
Chromatin
Gene Expression Regulation, Developmental
Genome
Internet
Lipids
Nerve Regeneration
Optic Nerve
Software
Zebrafish
