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Updated: Jan 10, 2026
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Differentially expressed genes and therapeutic targets for nonalcoholic fatty liver disease from transcriptomic
Jianing Li1, Yanan Li2, Yongsheng Zhang3
1Graduate School, Heilongjiang University of Traditional Chinese Medicine, Harbin, China.
Abstract:
Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver conditions globally. Lifestyle interventions are currently available as the main treatment modality. However, there is an urgent need to develop new therapeutic approaches for NAFLD owing to its complex pathological mechanisms. This study aimed to reveal potential therapeutic targets for NAFLD through molecular mechanism analysis. Using publicly available microarray datasets, we performed differentially expressed gene analysis to identify gene expression changes in NAFLD samples relative to healthy ones. Subsequently, expression-quantitative trait loci (eQTL) and Mendelian randomization (MR) analyses were applied to evaluate the relationship between these genes and NAFLD. Additionally, the potential functional pathways of differentially expressed genes were explored using enrichment analyses. A variety of differentially expressed genes are significantly up- or down-regulated in NAFLD samples. eQTL and MR analyses confirmed the causal relationship between some key genes and NAFLD. Enrichment analysis revealed that these genes are mainly associated with key signaling pathways, including inflammatory and immune responses, indicating that these pathways significantly contribute to the pathophysiology of NAFLD. This study revealed crucial genes and signaling pathways in NAFLD through multi-level bioinformatics and MR analysis, providing new insights for future treatments. The results underscore the necessity of comprehending NAFLD's intricate pathobiology to facilitate the development of innovative therapies, alleviate the burden on patients and society, and improve public health.
Insights
Nonalcoholic fatty liver disease (NAFLD) is a common condition needing new treatments. This study identified key genes and inflammatory pathways involved in NAFLD, offering potential new therapeutic targets.
Area of Science:
- Hepatology
- Genetics
- Bioinformatics
Background:
- Nonalcoholic fatty liver disease (NAFLD) is a prevalent global liver condition.
- Current treatments rely on lifestyle interventions, but new therapeutic strategies are needed due to complex NAFLD mechanisms.
Purpose of the Study:
- To identify potential therapeutic targets for NAFLD by analyzing molecular mechanisms.
- To reveal crucial genes and signaling pathways implicated in NAFLD pathogenesis.
Main Methods:
- Differential gene expression analysis of microarray datasets from NAFLD patients and healthy controls.
- Expression quantitative trait loci (eQTL) and Mendelian randomization (MR) analyses to assess gene-NAFLD relationships.
- Gene enrichment analyses to explore functional pathways.
Main Results:
- Identified numerous differentially expressed genes in NAFLD samples.
- Confirmed causal relationships between specific genes and NAFLD using eQTL and MR analyses.
- Revealed that key genes are associated with inflammatory and immune response pathways.
Conclusions:
- Multi-level bioinformatics and MR analyses identified critical genes and pathways in NAFLD.
- Findings provide novel insights into NAFLD pathobiology, supporting the development of innovative therapies.
- Understanding NAFLD's complexity is vital for effective treatment and public health improvement.
