TY - JOUR
T1 - Identification of key genes related to the prognosis of esophageal squamous cell carcinoma based on chip re-annotation
AU - Wang, Meiqi
AU - Liu, Dan
AU - Huang, Yunchuanxiang
AU - Jiang, Ziyi
AU - Wu, Feng
AU - Cen, Yu
AU - Ma, Lan
N1 - Funding Information:
This research was funded by Shenzhen Strategic Emerging Industry Development Special Funds, grant number JCYJ20170816143646446, and Shenzhen Science and Technology Research and Development Funds, grant number JCYJ20200109143018683. We thank Linyun Hong, Yang Yan, Wenning Cao, Chaowen Xue, Xiang Ji and Mingzhe Wang of the Lab for assistance during the study. We thank Tsinghua University for its generous support of necessary experiment instruments.
Funding Information:
Funding: This research was funded by Shenzhen Strategic Emerging Industry Development Special Funds, grant number JCYJ20170816143646446, and Shenzhen Science and Technology Research and Development Funds, grant number JCYJ20200109143018683.
Publisher Copyright:
© 2021 by the authors.
PY - 2021/4/1
Y1 - 2021/4/1
N2 - Esophageal cancer (EC) is one of the deadliest cancers worldwide. However, reliable biomarkers for early diagnosis, or those for the prognosis of therapy, remain unfulfilled goals for its subtype esophageal squamous cell carcinoma (ESCC). The purpose of this study was to identify reliable biomarkers for the diagnosis and prognosis of ESCC by gene chip re-annotation technique and downstream bioinformatics analysis. In our research, the GSE53624 dataset was downloaded from the GEO database. Then, we reannotated the gene expression probe and obtained the gene expression matrix. Differential expressed genes (DEGs) were found by R packages and they were subjected to Gene Ontology enrichment analysis and protein-protein interaction (PPI) network construction. As a result, a total of 28,885 mRNA probes were reannotated, among which 210 downregulated and 80 up-regulated DEGs were screened out. By combining these genes set in clinical prognosis information and Western blot analysis, we found four genes with diagnostic and prognostic significance, including MMP134SPP1, MMP10, and COL1A1. Furthermore, markers of infiltrating immune cells exhibited different DEG-related immune infiltration patterns.
AB - Esophageal cancer (EC) is one of the deadliest cancers worldwide. However, reliable biomarkers for early diagnosis, or those for the prognosis of therapy, remain unfulfilled goals for its subtype esophageal squamous cell carcinoma (ESCC). The purpose of this study was to identify reliable biomarkers for the diagnosis and prognosis of ESCC by gene chip re-annotation technique and downstream bioinformatics analysis. In our research, the GSE53624 dataset was downloaded from the GEO database. Then, we reannotated the gene expression probe and obtained the gene expression matrix. Differential expressed genes (DEGs) were found by R packages and they were subjected to Gene Ontology enrichment analysis and protein-protein interaction (PPI) network construction. As a result, a total of 28,885 mRNA probes were reannotated, among which 210 downregulated and 80 up-regulated DEGs were screened out. By combining these genes set in clinical prognosis information and Western blot analysis, we found four genes with diagnostic and prognostic significance, including MMP134SPP1, MMP10, and COL1A1. Furthermore, markers of infiltrating immune cells exhibited different DEG-related immune infiltration patterns.
KW - Bioinformatics analyses
KW - Chip re-annotation
KW - DEGs
KW - Esophageal squamous cell carcinoma
KW - Prognostic biomarkers
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U2 - 10.3390/app11073229
DO - 10.3390/app11073229
M3 - Article
AN - SCOPUS:85104058571
SN - 2076-3417
VL - 11
JO - Applied Sciences (Switzerland)
JF - Applied Sciences (Switzerland)
IS - 7
M1 - 3229
ER -