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

Joshua Orvis¹, Brian Gottfried¹, Jayaram Kancherla^{2

3

4}, Ricky S Adkins¹, Yang Song¹, Amiel A Dror^{5

6}, Dustin Olley¹, Kevin Rose⁷, Elena Chrysostomou⁷, Michael C Kelly⁸, Beatrice Milon⁷, Maggie S Matern⁷, Hela Azaiez⁹, Brian Herb¹, Carlo Colantuoni^{1

10}, Robert L Carter¹, Seth A Ament^{1

11}, Matthew W Kelley⁸, Owen White¹, Hector Corrada Bravo^{2

3

4}, Anup Mahurkar¹, Ronna Hertzano^{12

13

14}

Affiliations

¹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
² Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA.
³ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
⁴ Department of Computer Science, University of Maryland, College Park, MD, USA.
⁵ Department of Otolaryngology-Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel.
⁶ Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel.
⁷ Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.
⁸ Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.
⁹ Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, USA.
¹⁰ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
¹¹ Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
¹² Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.
¹³ Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.
¹⁴ Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.

PMID: 34172972
PMCID: PMC8996439
DOI: 10.1038/s41592-021-01200-9

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

Joshua Orvis et al. Nat Methods. 2021 Aug.

. 2021 Aug;18(8):843-844.

doi: 10.1038/s41592-021-01200-9.

Authors

Affiliations

¹ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
² Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA.
³ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
⁴ Department of Computer Science, University of Maryland, College Park, MD, USA.
⁵ Department of Otolaryngology-Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel.
⁶ Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel.
⁷ Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA.
⁸ Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.
⁹ Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, USA.
¹⁰ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
¹¹ Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
¹² Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.
¹³ Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.
¹⁴ Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA. rhertzano@som.umaryland.edu.

PMID: 34172972
PMCID: PMC8996439
DOI: 10.1038/s41592-021-01200-9

No abstract available

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Conflict of interest statement

Competing interests

The authors declare no competing interests.

Figures

**Fig. 1 |. gEAR overview.**
a, gEAR result page example. b, Users can select from a variety of custom displays. c, The scRNA-seq Analysis Workbench allows de novo analysis of a dataset; or, for datasets uploaded with expression metadata, analysis can start from marker gene identification and cluster comparison. d, The Compare tool identifies differentially expressed genes to generate gene carts. e, Additional features.

See this image and copyright information in PMC

References

1. Wilkinson MD et al. Sci. Data 3, 160018 (2016). - PMC - PubMed
1. Barrett T. et al. Nucleic Acids Res. 41, D991–D995 (2013). - PMC - PubMed
1. Cakir B. et al. NAR Genom. Bioinform 2, lqaa052 (2020). - PMC - PubMed
1. Chelaru F, Smith L, Goldstein N. & Bravo HC Nat. Methods 11, 938–940 (2014). - PMC - PubMed
1. Haeussler M. et al. Nucleic Acids Res. 47, D853–D858 (2019). (D1). - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources