基于蛋白的宫颈癌相关基因生物信息学分析

目的/意义 运用生物信息学方法挖掘与宫颈癌相关的基因,探讨与HPV E6/E7密切相关差异表达基因的特征及临床意义。方法/过程 以UCSC的TCGA和GTEx中宫颈癌的宫颈组织及临床信息作为训练集。以GEO中与宫颈癌相关的表达谱芯片GSE63514作为验证集。首先,使用R软件limma包筛选肿瘤和正常样本的DEGs,制作与MigDB中E6/E7蛋白相关基因的韦恩图。利用survival包进行生存分析,通过ROC和蛋白表达水平进行验证。其次,通过拷贝数变异和甲基化相关性得到关键基因。最后,构建特异性共表达网络并进行富集分析和免疫浸润分析。结果/结论 与HPV E6/E7蛋白相关的差异表达基因有101个,经筛选有3个基因意义显著,分别是E2F1、MCM4和PCNA。同时,经通路分析后发现特异性共表达网络中的基因显著富集在DNA复制、染色体组织等通路。通过免疫相关性分析发现关键基因与CD4 T细胞、B细胞和中性粒细胞显著相关。DNA复制、染色体组织等为宫颈鳞癌发生发展以及HPV E6/E7编码蛋白显著相关的分子机制和关键基因。

Protein-based Bioinformatics Analysis of Cervical Cancer Related Genes

Purpose/Significance To explore the characteristics and clinical significance of differentially expressed genes closely related to HPV E6/E7 by using bioinformatics.Method/Process The cervical tissue and clinical information of cervical cancer in TCGA and GTEx of UCSC are used as the training set. The expression profile chip GSE63514 related to cervical cancer in GEO is used as the validation set. Firstly, the limma package of R software is used to screen DEGs of tumor and normal samples, and Venn map of genes related to E6/E7 protein in MigDB is made. Survival analysis is performed by survival kit and verified by ROC and protein expression levels. Secondly, key genes are obtained by copy number variation and methylation correlation. Finally, the specific co-expression network is constructed and enrichment analysis and immune infiltration analysis are performed. Result/Conclusion There are 101 differentially expressed genes related to HPV E6/E7 protein, and three genes are found to have significance after screening, namely E2F1, MCM4 and PCNA. At the same time, it is found that the genes in the specific coexpression network are significantly enriched in the DNA replication and chromosome organization pathways.Immune correlation analysis shows that key genes are significantly associated with CD4 T cells, B cells and neutrophils. DNA replication, chromosome organization, etc., are the molecular mechanisms and key genes significantly related to the development of cervical squamous cell carcinoma and HPV E6/E7 encoded proteins.