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Less is more: relative rank is more informative than absolute abundance for compositional NGS data

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Publicado en:Briefings in Functional Genomics vol. 24 (2025)
Autor principal: Zheng, Xubin
Otros Autores: Jin, Nana, Wu, Qiong, Zhang, Ning, Wu, Haonan, Wang, Yuanhao, Luo, Rui, Liu, Tao, Ding, Wanfu, Geng, Qingshan, Cheng, Lixin
Publicado:
Oxford University Press
Materias:
Transcriptomes
Data processing
Data analysis
Biomarkers
Gene expression
Data integration
Research centers
Hospitals
Algorithms
Genomics
Geriatrics
Environmental
Acceso en línea:Citation/Abstract
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Resumen:High-throughput gene expression data have been extensively generated and utilized in biological mechanism investigations, biomarker detection, disease diagnosis and prognosis. These applications encompass not only bulk transcriptome, but also single cell RNA-seq data. However, extracting reliable biological information from transcriptome data remains challenging due to the constrains of Compositional Data Analysis. Current data preprocessing methods, including dataset normalization and batch effect correction, are insufficient to address these issues and improve data quality for downstream analysis. Alternatively, qualification methods focusing on the relative order of gene expression (ROGER) are more informative than the quantification methods that rely on gene expression abundance. The Pairwise Analysis of Gene expression method is an enhancement of ROGER, designed for data integration in either sample space or feature space. In this review, we summarize the methods applied to transcriptome data analysis and discuss their potentials in predicting clinical outcomes.
ISSN:2041-2649
2041-2657
1473-9550
DOI:10.1093/bfgp/elae045
Fuente:Health & Medical Collection