Brief Communication | Published:

SpatialDE: identification of spatially variable genes

Nature Methods volume 15, pages 343346 (2018) | Download Citation

Abstract

Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.

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Acknowledgements

The authors thank D. Arnol and F.P. Casale for helpful advice on statistics and data normalization. J. Moffitt helped us understand the data format for available MERFISH data. In addition, we thank A. Lun, M. Hemberg, D. Kunz, and K. Meyer for feedback on the manuscript. This work was supported by the EMBL (EMBL International PhD Program support to V.S.; core funding to O.S.), the Wellcome Trust (S.A.T. and O.S.), the ERC (Consolidator Grant “ThDEFINE” to S.A.T.), and the EU (O.S.).

Author information

Affiliations

  1. Wellcome Trust Sanger Institute, Hinxton, UK.

    • Valentine Svensson
    •  & Sarah A Teichmann
  2. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

    • Valentine Svensson
    •  & Oliver Stegle
  3. Theory of Condensed Matter Group, The Cavendish Laboratory, University of Cambridge, Cambridge, UK.

    • Sarah A Teichmann
  4. European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.

    • Oliver Stegle

Authors

  1. Search for Valentine Svensson in:

  2. Search for Sarah A Teichmann in:

  3. Search for Oliver Stegle in:

Contributions

V.S. and O.S. conceived the method. V.S. implemented the method and generated the results. V.S., S.A.T., and O.S. interpreted the results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Valentine Svensson or Oliver Stegle.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–15 and Supplementary Note 1

  2. 2.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Table 1

    Table with SpatialDE analysis results

Zip files

  1. 1.

    Supplementary Software

    SpatialDE Python package and usage examples, in addition to code and notebooks used to produce all results and figures.

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DOI

https://doi.org/10.1038/nmeth.4636