综合rna测序和网络分析方法鉴定与胃癌相关的枢纽基因和重要途径

IF 1.2 Q4 PHARMACOLOGY & PHARMACY
Karthick Vasudevan, Raghavendra B, Mithun A, Dhanushkumar T, Fazil Ahmad, Manoj Goyal, Monika Bansal, Tasneem Mohammed, Riyaz Ahmed Khan, Gayathri Pandurangam, George Priya Doss, Balu Kamaraj, Gurudeeban Selvaraj
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引用次数: 0

摘要

背景:胃癌是发展中国家最常见的癌症类型之一,在死亡原因中排名第四。幽门螺杆菌感染是胃癌发生的重要因素。缺乏早期诊断是胃癌死亡的主要原因。目的:明确胃癌发生的关键基因和通路。方法:本研究对人胃癌及邻近正常组织的RNA-Seq数据进行了综合分析。原始数据通过FastQC质量检查,并使用HISAT2与GRCh38对齐。Subread的featurecots处理转录本组装和量化。DESeq2定位了重要基因,ClueGO探索了基因本体和KEGG通路。利用StringApp构建蛋白-蛋白相互作用网络,通过CytoHubba帮助鉴定中心基因。这种整体的方法可以深入了解胃癌的分子机制。结果:本研究在正常和胃样本之间检测到711个差异表达基因(DEGs)。共鉴定出594个基因表达上调,117个基因表达下调。主要的deg在信号转导、刺激反应调节、跨膜信号受体活性和涉及细胞因子的信号转导通路中富集。此外,基于CytoHubba插件的MCC等级分析,从PPI网络中鉴定出20个枢纽基因,这些基因与胃癌的进展有关。结论:前6个中心基因CD4、CTLA4、CD28、CD80、CD27和SELL有望调控多种途径,并可能作为胃癌患者早期发现和治疗的潜在生物标志物。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Integrated RNA-sequencing and network analysis approach to identify the Hub genes and vital pathways associated with gastric cancer
Context: Gastric cancer is one of the most prevalent types of cancer in developing countries and ranks fourth in terms of death causes. Helicobacter pylori infection is a significant contributor to the emergence of gastric cancer. Lack of early diagnosis of gastric cancer is a leading cause of death. Aims: To identify the key genes and pathways involved in gastric cancer. Methods: This study performed a comprehensive analysis of RNA-Seq data from human gastric cancer and adjacent normal tissues. Raw data passed quality checks with FastQC and were aligned to GRCh38 using HISAT2. Subread's FeatureCounts handled transcript assembly and quantification. DESeq2 pinpointed significant genes, while ClueGO explored gene ontology and KEGG pathways. Protein-protein interaction networks, constructed with StringApp, aided in identifying hub genes through CytoHubba. This holistic approach yields insights into the molecular mechanisms underpinning gastric cancer. Results: This study detected 711 differentially expressed genes (DEGs) between normal and gastric samples. A total of 594 genes were identified as upregulated and 117 as downregulated. Major DEGs are enriched in signal transduction, stimulus-response regulation, transmembrane signaling receptor activity, and signal transduction pathways involving cytokines. In addition, 20 hub genes from the PPI network were identified based on MCC rank analysis from the CytoHubba plugin, contributing to the progression of gastric cancer. Conclusions: The top six hub genes, CD4, CTLA4, CD28, CD80, CD27, and SELL, are expected to regulate several pathways and may serve as potential biomarkers for the early detection and treatment of gastric cancer patients.
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来源期刊
CiteScore
3.00
自引率
20.00%
发文量
0
审稿时长
8 weeks
期刊介绍: The Journal of Pharmacy & Pharmacognosy Research (JPPRes) is an international, specialized and peer-reviewed open access journal, under the auspices of AVAGAX – Diseño, Publicidad y Servicios Informáticos, which publishes studies in the pharmaceutical and herbal fields concerned with the physical, botanical, chemical, biological, toxicological properties and clinical applications of molecular entities, active pharmaceutical ingredients, devices and delivery systems for drugs, vaccines and biologicals, including their design, manufacture, evaluation and marketing. This journal publishes research papers, reviews, commentaries and letters to the editor as well as special issues and review of pre-and post-graduate thesis from pharmacists or professionals involved in Pharmaceutical Sciences or Pharmacognosy.
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