An information theoretic approach to detecting spatially varying genes.

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_3A146C47077F
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
An information theoretic approach to detecting spatially varying genes.
Journal
Cell reports methods
Author(s)
Jones D.C., Danaher P., Kim Y., Beechem J.M., Gottardo R., Newell E.W.
ISSN
2667-2375 (Electronic)
ISSN-L
2667-2375
Publication state
Published
Issued date
26/06/2023
Peer-reviewed
Oui
Volume
3
Number
6
Pages
100507
Language
english
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
A key step in spatial transcriptomics is identifying genes with spatially varying expression patterns. We adopt an information theoretic perspective to this problem by equating the degree of spatial coherence with the Jensen-Shannon divergence between pairs of nearby cells and pairs of distant cells. To avoid the notoriously difficult problem of estimating information theoretic divergences, we use modern approximation techniques to implement a computationally efficient algorithm designed to scale with in situ spatial transcriptomics technologies. In addition to being highly scalable, we show that our method, which we call maximization of spatial information (Maxspin), improves accuracy across several spatial transcriptomics platforms and a variety of simulations when compared with a variety of state-of-the-art methods. To further demonstrate the method, we generated in situ spatial transcriptomics data in a renal cell carcinoma sample using the CosMx Spatial Molecular Imager and used Maxspin to reveal novel spatial patterns of tumor cell gene expression.
Keywords
Humans, Algorithms, Carcinoma, Renal Cell/genetics, Gene Expression Profiling, Technology, Kidney Neoplasms/genetics
Pubmed
Web of science
Open Access
Yes
Create date
13/07/2023 13:06
Last modification date
23/01/2024 7:23
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