Identifying Hub Genes and Pathways in Pancreatic Ductal Adenocarcinoma (PAAD): A comprehensive in silico study

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports Pub Date : 2025-01-22 DOI:10.1016/j.bbrep.2025.101921

Elham Karimi , Niloufar Sadat Kalaki , Seyed Mohammad Akrami

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引用次数: 0

Abstract

Background

One of the most aggressive tumors is pancreatic ductal adenocarcinoma (PAAD), which is usually discovered at an advanced stage and is linked to a poor response to current treatment options and a significant risk of metastasis.

Methods

The Gene Expression Omnibus (GEO) database selected GSE15471, GSE28735, GSE62165, and GSE16515. Differentially expressed genes (DEGs) were defined as having a logFC of >1 and ≤ −1 and an adjusted p-value of less than 0.05. Differentially expressed genes (DEGs) from the four datasets were identified using the GEO2R tool. KEGG and GO databases were used to identify related pathways. PPIs were analyzed using Cytoscape and Gephi. A GEPIA analysis confirmed the target genes.

Results

The analysis of protein-protein interactions (PPI) along with data from the Gene Expression Omnibus (GEO) led to the identification of 66 hub genes and 819 common differentially expressed genes (DEGs). GO and KEGG pathway analyses indicated that these DEGs are significantly associated with functions related to cell adhesion, extracellular exosomes, structural components of the extracellular matrix, and the cytoskeleton in muscle cells. The expression levels of 8 genes—FN1, CXCR4, MMP9, PXDN, CBS, ALB, GPT2, and EGF—demonstrated a notable difference between normal and tumor samples, as identified through GEPIA analysis.

Conclusion

The hub genes and related pathways that are connected to the development of PAAD were found in this study. These genes could serve as promising diagnostic biomarkers, offering a valuable chance to detect PAAD in its initial stages, leading to more effective treatment options.

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来源期刊

Biochemistry and Biophysics Reports Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

4.60

自引率

0.00%

发文量

191

审稿时长

59 days

期刊介绍： Open access, online only, peer-reviewed international journal in the Life Sciences, established in 2014 Biochemistry and Biophysics Reports (BB Reports) publishes original research in all aspects of Biochemistry, Biophysics and related areas like Molecular and Cell Biology. BB Reports welcomes solid though more preliminary, descriptive and small scale results if they have the potential to stimulate and/or contribute to future research, leading to new insights or hypothesis. Primary criteria for acceptance is that the work is original, scientifically and technically sound and provides valuable knowledge to life sciences research. We strongly believe all results deserve to be published and documented for the advancement of science. BB Reports specifically appreciates receiving reports on: Negative results, Replication studies, Reanalysis of previous datasets.