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gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

Joshua Orvis, Brian Gottfried, Jayaram Kancherla, Ricky S. Adkins, Yang Song, Amiel A. Dror, Dustin Olley, Kevin Rose, Elena Chrysostomou, Michael C. Kelly, Beatrice Milon, Maggie S. Matern, Hela Azaiez, Brian Herb, Carlo Colantuoni, Robert L. Carter, Seth A. Ament, Matthew W. Kelley, Owen White, Hector Corrada Bravo, Anup Mahurkar, Ronna Hertzano
doi: https://doi.org/10.1101/2020.08.28.272039
Joshua Orvis
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Brian Gottfried
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Jayaram Kancherla
2Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
4Department of Computer Science, University of Maryland, College Park, MD 20742, USA
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Ricky S. Adkins
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Yang Song
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Amiel A. Dror
5Department of Otolaryngology-Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel
6Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
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Dustin Olley
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Kevin Rose
7Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore 21201, USA
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Elena Chrysostomou
7Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore 21201, USA
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Michael C. Kelly
8Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
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Beatrice Milon
7Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore 21201, USA
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Maggie S. Matern
7Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore 21201, USA
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Hela Azaiez
9Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, Iowa 52242, USA
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Brian Herb
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Carlo Colantuoni
10Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Robert L. Carter
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Seth A. Ament
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Matthew W. Kelley
8Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
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Owen White
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Hector Corrada Bravo
2Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
3Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
4Department of Computer Science, University of Maryland, College Park, MD 20742, USA
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Anup Mahurkar
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Ronna Hertzano
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
7Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore 21201, USA
11Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore 21201, USA
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  • For correspondence: rhertzano@som.umaryland.edu
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ABSTRACT

The gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data types (bulk, sorted, single cell/nucleus) and epigenomics data, from multiple species, time points and tissues in a single-page, user-friendly browsable format. An integrated scRNA-seq workbench provides access to raw data of scRNA-seq datasets for de novo analysis, as well as marker-gene and cluster comparisons of pre-assigned clusters. Users can upload, view, analyze and privately share their own data in the context of previously published datasets. Short, permanent URLs can be generated for dissemination of individual or collections of datasets in published manuscripts. While the gEAR is currently curated for auditory research with over 90 high-value datasets organized in thematic profiles, the gEAR also supports the BRAIN initiative (via nemoanalytics.org) and is easily adaptable for other research domains.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://umgear.org

  • https://github.com/IGS/gEAR/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
Joshua Orvis, Brian Gottfried, Jayaram Kancherla, Ricky S. Adkins, Yang Song, Amiel A. Dror, Dustin Olley, Kevin Rose, Elena Chrysostomou, Michael C. Kelly, Beatrice Milon, Maggie S. Matern, Hela Azaiez, Brian Herb, Carlo Colantuoni, Robert L. Carter, Seth A. Ament, Matthew W. Kelley, Owen White, Hector Corrada Bravo, Anup Mahurkar, Ronna Hertzano
bioRxiv 2020.08.28.272039; doi: https://doi.org/10.1101/2020.08.28.272039
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gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
Joshua Orvis, Brian Gottfried, Jayaram Kancherla, Ricky S. Adkins, Yang Song, Amiel A. Dror, Dustin Olley, Kevin Rose, Elena Chrysostomou, Michael C. Kelly, Beatrice Milon, Maggie S. Matern, Hela Azaiez, Brian Herb, Carlo Colantuoni, Robert L. Carter, Seth A. Ament, Matthew W. Kelley, Owen White, Hector Corrada Bravo, Anup Mahurkar, Ronna Hertzano
bioRxiv 2020.08.28.272039; doi: https://doi.org/10.1101/2020.08.28.272039

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