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Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses.
Han, Gang; Yan, Dongyan; Sun, Zhe; Fang, Jiyuan; Chang, Xinyue; Wilson, Lucas; Liu, Yushi.
Afiliación
  • Han G; Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA.
  • Yan D; Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
  • Sun Z; Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
  • Fang J; Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
  • Chang X; Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
  • Wilson L; Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA.
  • Liu Y; Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA. liu_yushi@lilly.com.
Hum Genomics ; 18(1): 69, 2024 Jun 20.
Article en En | MEDLINE | ID: mdl-38902839
ABSTRACT

BACKGROUND:

Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive.

RESULTS:

Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study.

CONCLUSION:

In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Teorema de Bayes / Análisis de Secuencia de ARN / Análisis de la Célula Individual / RNA-Seq Límite: Humans Idioma: En Revista: Hum Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Teorema de Bayes / Análisis de Secuencia de ARN / Análisis de la Célula Individual / RNA-Seq Límite: Humans Idioma: En Revista: Hum Genomics Asunto de la revista: GENETICA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido