Dysregulated ligand-receptor interactions from single-cell transcriptomics.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
13 06 2022
13 06 2022
Historique:
received:
16
06
2021
revised:
29
03
2022
accepted:
21
04
2022
pubmed:
29
4
2022
medline:
15
11
2022
entrez:
28
4
2022
Statut:
ppublish
Résumé
Intracellular communication is crucial to many biological processes, such as differentiation, development, homeostasis and inflammation. Single-cell transcriptomics provides an unprecedented opportunity for studying cell-cell communications mediated by ligand-receptor interactions. Although computational methods have been developed to infer cell type-specific ligand-receptor interactions from one single-cell transcriptomics profile, there is lack of approaches considering ligand and receptor simultaneously to identifying dysregulated interactions across conditions from multiple single-cell profiles. We developed scLR, a statistical method for examining dysregulated ligand-receptor interactions between two conditions. scLR models the distribution of the product of ligands and receptors expressions and accounts for inter-sample variances and small sample sizes. scLR achieved high sensitivity and specificity in simulation studies. scLR revealed important cytokine signaling between macrophages and proliferating T cells during severe acute COVID-19 infection, and activated TGF-β signaling from alveolar type II cells in the pathogenesis of pulmonary fibrosis. scLR is freely available at https://github.com/cyhsuTN/scLR. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 35482476
pii: 6575434
doi: 10.1093/bioinformatics/btac294
pmc: PMC9191214
doi:
Substances chimiques
Ligands
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
3216-3221Subventions
Organisme : NCI NIH HHS
ID : U54 CA217450
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA095103
Pays : United States
Organisme : NCI NIH HHS
ID : U19 CA179514
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA098131
Pays : United States
Organisme : NCI NIH HHS
ID : P01 CA229123
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA091842
Pays : United States
Organisme : NIAID NIH HHS
ID : P01 AI139449
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA068485
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA236733
Pays : United States
Informations de copyright
© The Author(s) 2022. Published by Oxford University Press.
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