Assessing RNA-Seq Workflow Methodologies Using Shannon Entropy

• Published in: Biology (Basel, Switzerland) Vol. 13; no. 7; p. 482
• Main Author: Carels, Nicolas
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28.06.2024
• Subjects: benchmarking; Binomial distribution; Cancer; Data processing; Entropy; Gene expression; median normalization; Methods; mRNA; Nonparametric statistics; PPI network; RNA processing; RPKM; Survival; Tumors; median normalization; PPI network; entropy; benchmarking; RPKM; 5-year OS; cancer
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology13070482

RNA-seq faces persistent challenges due to the ongoing, expanding array of data processing workflows, none of which have yet achieved standardization to date. It is imperative to determine which method most effectively preserves biological facts. Here, we used Shannon entropy as a tool for depicting the biological status of a system. Thus, we assessed the measurement of Shannon entropy by several RNA-seq workflow approaches, such as DESeq2 and edgeR, but also by combining nine normalization methods with log fold change on paired samples of TCGA RNA-seq representing datasets of 515 patients and spanning 12 different cancer types with 5-year overall survival rates ranging from 20% to 98%. Our analysis revealed that TPM, RLE, and TMM normalization, coupled with a threshold of log fold change ≥1, for identifying differentially expressed genes, yielded the best results. We propose that Shannon entropy can serve as an objective metric for refining the optimization of RNA-seq workflows and mRNA sequencing technologies.