Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
05 May 2023
05 May 2023
Historique:
accepted:
22
04
2023
revised:
24
03
2023
received:
17
11
2022
medline:
5
5
2023
pubmed:
5
5
2023
entrez:
5
5
2023
Statut:
aheadofprint
Résumé
The study of cellular networks mediated by ligand-receptor interactions has attracted much attention recently owing to single-cell omics. However, rich collections of bulk data accompanied with clinical information exists and continue to be generated with no equivalent in single-cell so far. In parallel, spatial transcriptomic (ST) analyses represent a revolutionary tool in biology. A large number of ST projects rely on multicellular resolution, for instance the Visium™ platform, where several cells are analyzed at each location, thus producing localized bulk data. Here, we describe BulkSignalR, a R package to infer ligand-receptor networks from bulk data. BulkSignalR integrates ligand-receptor interactions with downstream pathways to estimate statistical significance. A range of visualization methods complement the statistics, including functions dedicated to spatial data. We demonstrate BulkSignalR relevance using different datasets, including new Visium liver metastasis ST data, with experimental validation of protein colocalization. A comparison with other ST packages shows the significantly higher quality of BulkSignalR inferences. BulkSignalR can be applied to any species thanks to its built-in generic ortholog mapping functionality.
Identifiants
pubmed: 37144485
pii: 7152875
doi: 10.1093/nar/gkad352
pmc: PMC10250239
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : J.C.
ID : INCa R17080FF-CT
Organisme : Fondation ARC pour la Recherche sur le Cancer
ID : PJA 20141201975
Organisme : Région Occitanie, programme Recherche et Société(s)
Organisme : European Union
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
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