Method for screening immune infiltration related prognostic genes in breast cancer tumor microenvironment
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A technology related to breast cancer tumors and immunity, applied in the field of screening immune infiltration-related prognosis genes in the microenvironment of breast cancer tumors
Inactive Publication Date: 2020-11-03
NANJING UNIV OF POSTS & TELECOMM
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Although the study of tumor immune microenvironment-related genes plays an important role i
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Embodiment 1
[0024] Such as figure 1 As shown, a method for screening prognostic genes related to immune infiltration in the tumor microenvironment of breast cancer, including:
[0025] Step 1) download the gene expression data (TCGA-BRCA) and relevant clinical information of breast cancer in the TCGA database, and download 3 breast cancer related GEO datasets from GEO;
[0026] Step 2) Perform estimate analysis on the TCGA-BRCA data set, group the obtained immune-related gene score data according to high and low scores, and then use the limma package to perform differential expression analysis;
[0027] Step 3) Perform batch correction on the 3 GEO data sets, merge them into one batch of data, and expand the analysis sample size;
[0028] Step 4) Perform estimate analysis based on the batch results obtained in step 3), group the obtained immune-related gene score data into high and low scores, and then use the limma package to perform differential expression analysis.
[0029] Step 5) A...
Embodiment 2
[0046] A method for screening immune infiltration-related prognosis genes in the tumor microenvironment of breast cancer, the specific content comprising:
[0047]1. Prepare the data set to be analyzed. Firstly, the breast cancer (BRCA) transcriptome data (1,109 cases of cancer tissue and 113 cases of normal tissue) and corresponding clinical data sets were downloaded from the TCGA (The Cancer Genome Atlas) database, and then downloaded from the GEO (Gene Expression Omnibus database) Screen and collect breast cancer transcriptome data sets in the database, including GSE38959 (30 cancer tissues, 13 normal tissues), GSE45827 (130 cancer tissues, 11 normal tissues), GSE65194 (153 cancer tissues, 11 normal tissues ).
[0048] 2. Analyze the data set and screen the prognostic genes related to tumor immune infiltration in BRCA, which is mainly divided into three steps: the first step is to analyze the tumor immune-related genes through the estimate algorithm on the data set obtaine...
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Abstract
The invention belongs to the technical field of medicines, and particularly relates to a method for screening immune infiltration related prognostic genes in a breast cancer tumor microenvironment. The method comprises the following steps of performing tumor immune related gene analysis on a TCGA-BRCA data set and 3 GEO transcriptome data sets subjected to batch correction through an estimate algorithm, and grouping obtained immune related gene score data according to high and low scores; performing differential expression analysis; taking an intersection of differential expression analysis results obtained by the TCGA-BRCA data set and the GEO transcriptome data sets; and performing single-factor cox regression analysis on the intersection result of the TCGA-BRCA data set and the GEO transcriptome data sets by combining clinical data, performing lasso regression analysis, performing multi-factor cox regression analysis, and finally, performing survival analysis to obtain the breast cancer immune infiltration related prognostic gene. The breast cancer immune infiltration prognosis related gene with high reliability screened based on the method can provide effective information fordiagnosis and treatment of breast cancer.
Description
technical field [0001] The invention belongs to the technical field of medicine, and in particular relates to a method for screening prognosis genes related to immune infiltration in the tumor microenvironment of breast cancer. Background technique [0002] Breast cancer is one of the most common malignant tumors in the world. It is a malignant tumor that occurs in the glandular epithelial tissue of the breast. Its morbidity and mortality have been on the rise, and it has become a common tumor that threatens women's physical and mental health. [0003] In recent years, increasing evidence has shown that tumor immunity-related genes play important roles in various human cancers. In some cases, immune cells not only fail to function as anti-tumor effectors, but may also promote tumor growth. Therefore, it is very important to screen key immune-related genes and conduct targeted research. Although the study of tumor immune microenvironment-related genes plays an important rol...
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