Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data

There is growing attention toward closed biological genomes in the environment and in health. To explore and reveal the intergroup differences among different samples or environments, it is crucial to discover biomarkers with statistical differences among groups. The application of Linear discrimina...

Celý popis

Uloženo v:
Podrobná bibliografie
Vydáno v:Journal of visualized experiments číslo 183
Hlavní autoři: Chang, Fang, He, Shishi, Dang, Chenyuan
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 16.05.2022
Témata:
biomarkers
Biomarkers - analysis
Discriminant Analysis
genome
genomics
microbiome
Microbiota - genetics
Quality Control
ISSN:1940-087X, 1940-087X
On-line přístup:Získat plný text
Tagy: Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
Popis
Shrnutí:There is growing attention toward closed biological genomes in the environment and in health. To explore and reveal the intergroup differences among different samples or environments, it is crucial to discover biomarkers with statistical differences among groups. The application of Linear discriminant analysis Effect Size (LEfSe) can help find good biomarkers. Based on the original genome data, quality control, and quantification of different sequences based on taxa or genes are carried out. First, the Kruskal-Wallis rank test was used to distinguish between specific differences among statistical and biological groups. Then, the Wilcoxon rank test was performed between the two groups obtained in the previous step to assess whether the differences were consistent. Finally, a linear discriminant analysis (LDA) was conducted to evaluate the influence of biomarkers on significantly different groups based on LDA scores. To sum up, LEfSe provided the convenience for identifying genomic biomarkers that characterize statistical differences among biological groups.
Bibliografie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ObjectType-Correction/Retraction-4
ObjectType-Undefined-3
ISSN:1940-087X
1940-087X
DOI:10.3791/61715