Lv Xiaofei, Yu Xi
Department of Stomatology, The Second Hospital of Tianjin Medical University, Tianjin, China.
Department of Anesthesiology, The Second Hospital of Tianjin Medical University, Tianjin, China.
Front Surg. 2023 Jan 4;9:952389. doi: 10.3389/fsurg.2022.952389. eCollection 2022.
Tongue cancer, as one of the most malignant oral cancers, is highly invasive and has a high risk of recurrence. At present, tongue cancer is not obvious and easy to miss the opportunity for early diagnosis when in the advanced stage. It is important to find markers that can predict the occurrence and progression of tongue cancer.
Bioinformatics analysis plays an important role in the acquisition of marker genes. GEO and TCGA data are very important public databases. In addition to expression data, the TCGA database also contains corresponding clinical data. In this study, we screened three GEO data sets that met the standard, which included GSE13601, GSE34105, and GSE34106. These data sets were combined using the SVA package to prepare the data for differential expression analysis, and then the limma package was used to set the standard to < 0.05 and |log2 (FC)| ≥ 1.5.
A total of 170 differentially expressed genes (DEGs) were identified. In addition, the DEseq package was used for differential expression analysis using the same criteria for samples in the TCGA database. It ended up with 1,589 DEGs (644 upregulated, 945 downregulated). By merging these two sets of DEGs, 5 common upregulated DEGs (, , , , and ) and 15 common downregulated DEGs were obtained.
Further functional analysis of the DEGs showed that , , and are closely related to prognosis and may be a therapeutic target of TSCC.
舌癌作为最具侵袭性的口腔癌之一，具有高度侵袭性且复发风险高。目前，舌癌在晚期时症状不明显，容易错过早期诊断的机会。寻找能够预测舌癌发生和进展的标志物非常重要。
生物信息学分析在获取标志物基因方面发挥着重要作用。GEO和TCGA数据是非常重要的公共数据库。除了表达数据外，TCGA数据库还包含相应的临床数据。在本研究中，我们筛选出了三个符合标准的GEO数据集，分别为GSE13601、GSE34105和GSE34106。使用SVA软件包对这些数据集进行合并，为差异表达分析准备数据，然后使用limma软件包将标准设定为<0.05且|log2(FC)|≥1.5。
共鉴定出170个差异表达基因（DEG）。此外，使用DEseq软件包对TCGA数据库中的样本按照相同标准进行差异表达分析。最终得到1589个DEG（644个上调，945个下调）。通过合并这两组DEG，获得了5个共同上调的DEG（、、、和）和15个共同下调的DEG。
对DEG的进一步功能分析表明，、和与预后密切相关，可能是舌鳞状细胞癌的治疗靶点。
