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Regeneration Rosetta : an interactive web application to explore regeneration-associated gene expression and chromatin accessibility

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.
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https://hal.inrae.fr/hal-02625234
Contributor : Migration Prodinra <>
Submitted on : Tuesday, May 26, 2020 - 1:52:54 PM
Last modification on : Tuesday, June 15, 2021 - 2:56:14 PM

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Andrea Rau, Sumona P. Dhara, Ava J. Udvadia, Paul L. Auer. Regeneration Rosetta : an interactive web application to explore regeneration-associated gene expression and chromatin accessibility. G3, Genetics Society of America, 2019, 9 (12), pp.3953-3959. ⟨10.1534/g3.119.400729⟩. ⟨hal-02625234⟩

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