Skip to main content
SpringerLink
Log in

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

  • Correspondence
  • Published:

From Nature Methods

View current issue Submit your manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1: gEAR overview.

Code availability

The gEAR code is available on GitHub (https://github.com/IGS/gEAR) or Zenodo (https://doi.org/10.5281/zenodo.4818596) and released under the GNU Affero General Public License v3.0.

References

  1. Wilkinson, M. D. et al. Sci. Data 3, 160018 (2016).

    Article  Google Scholar 

  2. Barrett, T. et al. Nucleic Acids Res. 41, D991–D995 (2013).

    Article  CAS  Google Scholar 

  3. Cakir, B. et al. NAR Genom. Bioinform. 2, lqaa052 (2020).

    Article  Google Scholar 

  4. Chelaru, F., Smith, L., Goldstein, N. & Bravo, H. C. Nat. Methods 11, 938–940 (2014).

    Article  CAS  Google Scholar 

  5. Haeussler, M. et al. Nucleic Acids Res. 47, D853–D858 (2019). (D1).

    Article  CAS  Google Scholar 

  6. Pruitt, K. D. et al. Genome Res. 19, 1316–1323 (2009).

    Article  CAS  Google Scholar 

  7. Cunningham, F. et al. Nucleic Acids Res. 47, D745–D751 (2019).

    Article  CAS  Google Scholar 

  8. McKusick, V. A. Am. J. Hum. Genet. 80, 588–604 (2007).

    Article  CAS  Google Scholar 

  9. Moffitt, J. R. et al. Proc. Natl Acad. Sci. USA 113, 11046–11051 (2016).

    Article  CAS  Google Scholar 

  10. Marx, V. Nat. Methods 18, 9–14 (2021).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to the members of the Hearing Restoration Project for serving as the focus group in developing this tool and their continuous feedback. We thank R. Marini for technical assistance. This work was funded by the Hearing Restoration Project (R.H.); R01-DC013817 and R01-DC019370 (R.H.); R24- 96MH114815 (R.H. and O.W.); and R01-GM114267 (H.C.B).

Author information

Authors and Affiliations

  1. Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

    Joshua Orvis, Brian Gottfried, Ricky S. Adkins, Yang Song, Dustin Olley, Brian Herb, Carlo Colantuoni, Robert L. Carter, Seth A. Ament, Owen White, Anup Mahurkar & Ronna Hertzano

  2. Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA

    Jayaram Kancherla & Hector Corrada Bravo

  3. Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA

    Jayaram Kancherla & Hector Corrada Bravo

  4. Department of Computer Science, University of Maryland, College Park, MD, USA

    Jayaram Kancherla & Hector Corrada Bravo

  5. Department of Otolaryngology–Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel

    Amiel A. Dror

  6. Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel

    Amiel A. Dror

  7. Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, USA

    Kevin Rose, Elena Chrysostomou, Beatrice Milon, Maggie S. Matern & Ronna Hertzano

  8. Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA

    Michael C. Kelly & Matthew W. Kelley

  9. Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, USA

    Hela Azaiez

  10. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Carlo Colantuoni

  11. Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA

    Seth A. Ament

  12. Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA

    Ronna Hertzano

Authors
  1. Joshua Orvis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brian Gottfried
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jayaram Kancherla
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ricky S. Adkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yang Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Amiel A. Dror
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dustin Olley
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Kevin Rose
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Elena Chrysostomou
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Michael C. Kelly
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Beatrice Milon
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Maggie S. Matern
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Hela Azaiez
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Brian Herb
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Carlo Colantuoni
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Robert L. Carter
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Seth A. Ament
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Matthew W. Kelley
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Owen White
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Hector Corrada Bravo
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Anup Mahurkar
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Ronna Hertzano
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Portal design: J.O., B.G., R.S.A., A.M. and R.H. Data archive and infrastructure: J.O., B.G., R.S.A., J.K., M.C.K., H.C.B., S.A.A., C.C., B.H., O.W. and A.M. Graphic design: A.A.D. User interface: J.O., B.G., R.S.A., D.O. and A.M. User manual: J.O., Y.S., K.R., E.C. and R.H. DVD and deafness gene/locus integration: H.A., J.O, and R.H. Providing unpublished data: K.R., M.C.K, M.W.K. and R.H. Project management: R.L.C., A.M. and R.H. Data upload and analysis: J.O., D.O., Y.S., E.C., B.M., M.S.M. and R.H. Writing the manuscript: J.O., B.M., A.M. and R.H.

Corresponding author

Correspondence to Ronna Hertzano.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Methods thanks Eran Mukamel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Orvis, J., Gottfried, B., Kancherla, J. et al. gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. Nat Methods 18, 843–844 (2021). https://doi.org/10.1038/s41592-021-01200-9

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41592-021-01200-9

  • Springer Nature America, Inc.

This article is cited by

Search

Navigation