XPA-Express: A Python-Based Tool for Transcriptomic Data Analysis with Application to DNA Repair Deficiency

DNA repair mechanisms are essential for maintaining genome integrity and preventing genetic instability, which contributes to various diseases, including cancer, aging, and neurodegenerative disorders. Among these pathways, nucleotide excision repair (NER) plays a crucial role in damage recognition and the recruitment of repair components. Deficiencies in DNA repair pathways, such as those involving the xeroderma pigmentosum group A (XPA) protein, compromise repair capacity, leading to hypersensitivity to ultraviolet (UV) radiation and increased cancer susceptibility. Despite the established role of XPA in DNA repair, its broader impact on transcriptional regulation remains underexplored. To address this, we developed a Python-based tool that automates the retrieval, preprocessing, and differential expression (DE) analysis of RNA-seq data. In this study, we applied the tool to the GEO dataset GSE۱۰۰۸۵۵, which consists of ۴۸ samples with different XPA statuses. The analysis identified differentially expressed genes, including STK۲۶, PDE۸B, and CYP۴F۳, which exhibited significant changes in expression. These findings illustrate how DNA repair deficiencies, specifically related to XPA, can alter transcriptional programs and demonstrate the utility of this tool for transcriptomic analysis in the context of DNA repair.

کلیدواژه ها:

RNA-Seq ، differential expression ، DNA Repair ، Transcriptional regulation ، XPA ، NER