HiDeF: identifying persistent structures in multiscale 'omics data.
Community detection
Multiscale
Persistent homology
Protein-protein interaction network
Resolution
Single-cell clustering
Systems biology
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
07 01 2021
07 01 2021
Historique:
received:
25
06
2020
accepted:
08
12
2020
entrez:
8
1
2021
pubmed:
9
1
2021
medline:
20
1
2021
Statut:
epublish
Résumé
In any 'omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here, we use the concept of persistent homology, drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.
Identifiants
pubmed: 33413539
doi: 10.1186/s13059-020-02228-4
pii: 10.1186/s13059-020-02228-4
pmc: PMC7789082
doi:
Substances chimiques
Viral Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
21Subventions
Organisme : NIH HHS
ID : P41 GM103712
Pays : United States
Organisme : NIH HHS
ID : R01 HG009979
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103504
Pays : United States
Organisme : NIDDK NIH HHS
ID : P01 DK096990
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM103712
Pays : United States
Organisme : NIH HHS
ID : P01 DK096990
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009979
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209891
Pays : United States
Organisme : NIH HHS
ID : U54 CA209891
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA184427
Pays : United States
Commentaires et corrections
Type : UpdateOf
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