Screen of key characteristic genes of ESCC base on machine learning, analysis of immune cell infiltration and prediction of traditional Chinese medicine
SONG Yun-sheng,BAI Xiang-yu,YANG Zhi-peng
Abstract:
Objective Explore the potential targets and pathogenesis of esophageal squamous cell carcinoma(ESCC), and further use bioinformatics technology to predict potential traditional Chinese medicine treatments for ESCC. Methods ESCC gene chip was obtained by searching GEO database, and the different genes were screened. Perform Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on differentially expressed genes using the R software "colorsESCCe, stringi, ggplot2, Bioconductor". Using the R software "e1071, preprocessCore", the differential genes obtained were subjected to infiltration analysis on 22 types of immune cells based on the CIBERSORT algorithm, and the correlation between immune infiltration cells and characteristic genes was analyzed. Retrieve potential traditional Chinese medicine for characteristic gene therapy of ESCC through Coremine and Herb databases. Results Obtained 4 characteristic genes for ESCC, including UBL3, KIF4A, KIF14, and GPX3. The results of immune cell infiltration analysis showed that CD4+T cells, M0 macrophages, M2 macrophages, and activated dendritic cells were significantly upregulated in ESCC patients; Resting mast cells and activated mast cells were significantly downregulated. Chinese herbal medicines such as salvia miltiorrhiza, citron, saffron, gouqizi, poria cocos, ginseng, biejia are potential drugs for ESCC. Conclusion The characteristic genes are related to the progress of ESCC, and it is predicted that traditional Chinese medicines such as Salvia miltiorrhiza, grapefruit, saffron, gouqizi, poria cocos, ginseng and turtle shell may be potential drugs for the treatment of ESCC with targeted characteristic genes. This provides a new direction for the clinical diagnosis, treatment, and drug development of ESCC, and is expected to bring more accurate and effective treatment methods to ESCC patients.
