Inferring cellular heterogeneity of associations from single cell genomics.
Bioinformatics
; 36(11): 3466-3473, 2020 06 01.
Article
em En
| MEDLINE
| ID: mdl-32129824
ABSTRACT
MOTIVATION Cell-to-cell variation has uncovered associations between cellular phenotypes. However, it remains challenging to address the cellular diversity of such associations. RESULTS:
Here, we do not rely on the conventional assumption that the same association holds throughout the entire cell population. Instead, we assume that associations may exist in a certain subset of the cells. We developed CEllular Niche Association (CENA) to reliably predict pairwise associations together with the cell subsets in which the associations are detected. CENA does not rely on predefined subsets but only requires that the cells of each predicted subset would share a certain characteristic state. CENA may therefore reveal dynamic modulation of dependencies along cellular trajectories of temporally evolving states. Using simulated data, we show the advantage of CENA over existing methods and its scalability to a large number of cells. Application of CENA to real biological data demonstrates dynamic changes in associations that would be otherwise masked. AVAILABILITY AND IMPLEMENTATION CENA is available as an R package at Github https//github.com/mayalevy/CENA and is accompanied by a complete set of documentations and instructions. CONTACT iritgv@gmail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Genômica
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2020
Tipo de documento:
Article
País de afiliação:
Israel