Transcriptomic Analysis Based on Bulk RNA-seq Data

Nonalcoholic fatty liver (NAFL) is usually considered a benign condition; however, once it progresses to non-alcoholic steatohepatitis (NASH), patients face a significantly elevated risk of developing end-stage liver disease. Many studies are attempting to elucidate the molecular mechanism underlying the transition from NAFL to NASH. High-throughput sequencing technologies (such as bulk RNA-seq) have provided researchers with a deeper understanding by examining the transcriptome, revealing the expression of molecules, activation of signaling pathways, and other factors associated with disease progression. There is a wealth of open-source data available for researchers to analyze in order to identify potential targets for disease treatment. However, related research is limited by the lack of an efficient and reliable process for upstream analysis of the transcriptome. Here, a highly reproducible and user-friendly upstream analysis and subsequent related differential gene analysis pipeline is provided to achieve standardized processing and deep parsing of private or public data. The pipeline is divided into four steps: (1) quality control of data; (2) gene mapping; (3) differential gene analysis; and (4) functional analysis. This process aims to uncover the molecular mechanisms of disease transformation and assist researchers in screening potential drug targets and therapeutic approaches through the analysis of Bulk RNA-seq data.