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Gaussian embedding for large-scale gene set analysis

Nature Machine Intelligence volume 2, pages 387–395 (2020)Cite this article

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Abstract

Gene sets, including protein complexes and signalling pathways, have proliferated greatly, in large part as a result of high-throughput biological data. Leveraging gene sets to gain insight into biological discovery requires computational methods for converting them into a useful form for available machine learning models. Here, we study the problem of embedding gene sets as compact features that are compatible with available machine learning codes. We present Set2Gaussian, a novel network-based gene set embedding approach, which represents each gene set as a multivariate Gaussian distribution rather than a single point in the low-dimensional space, according to the proximity of these genes in a protein–protein interaction network. We demonstrate that Set2Gaussian improves gene set member identification, accurately stratifies tumours, and finds concise gene sets for gene set enrichment analysis. We further show how Set2Gaussian allows us to identify a clinical prognostic and predictive subnetwork around neurofilament medium in sarcoma, which we validate in independent cohorts.

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Fig. 1: Overview of Set2Gaussian.
Fig. 2: Application of Set2Gaussian to gene set member identification.
Fig. 3: Application of Set2Gaussian to cancer subtyping.
Fig. 4: Application of Set2Gaussian to finding concise gene sets.

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Data availability

We provide pretrained gene set representations of all gene sets in NCI, Reactome and MSigDB at https://doi.org/10.6084/m9.figshare.11341181.v1. All results in this paper are based on these representations.

Code availability

A software implementation of Set2Gaussian is is available at https://doi.org/10.5281/zenodo.3827929.

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Acknowledgements

This work is supported by NIH TR002515, GM102365, LM005652 and the Chan-Zuckerberg Biohub.

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Authors and Affiliations

  1. Department of Bioengineering, Stanford University, Stanford, CA, USA

    Sheng Wang & Russ B. Altman

  2. Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA

    Emily R. Flynn & Russ B. Altman

  3. Department of Genetics, Stanford University, Stanford, CA, USA

    Russ B. Altman

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  1. Sheng Wang
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  2. Emily R. Flynn
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All authors conceived the problem. S.W. conceived the algorithm and performed the computational experiments. R.B.A. led the research. All authors wrote the manuscript.

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Correspondence to Russ B. Altman.

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R.B.A. declares the following competing interests: stock or other ownership (Personalis, 23andme, Youscript) and consulting or advisory roles (United Health, Second Genome, Karius, UK Biobank, Swiss Personalized Health Network).

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Wang, S., Flynn, E.R. & Altman, R.B. Gaussian embedding for large-scale gene set analysis. Nat Mach Intell 2, 387–395 (2020). https://doi.org/10.1038/s42256-020-0193-2

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