An information theoretic approach to detecting spatially varying genes.

Détails

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Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_3A146C47077F
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
An information theoretic approach to detecting spatially varying genes.
Périodique
Cell reports methods
Auteur⸱e⸱s
Jones D.C., Danaher P., Kim Y., Beechem J.M., Gottardo R., Newell E.W.
ISSN
2667-2375 (Electronic)
ISSN-L
2667-2375
Statut éditorial
Publié
Date de publication
26/06/2023
Peer-reviewed
Oui
Volume
3
Numéro
6
Pages
100507
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Résumé
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.
Mots-clé
Humans, Algorithms, Carcinoma, Renal Cell/genetics, Gene Expression Profiling, Technology, Kidney Neoplasms/genetics
Pubmed
Web of science
Open Access
Oui
Création de la notice
13/07/2023 14:06
Dernière modification de la notice
23/01/2024 8:23
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