Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI’s Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis

Yu-Jing, Tan; Tang, Wenjing; Tang, Biao

doi:10.12659/msm.923934

Cited by 8 publications

(7 citation statements)

References 60 publications

(62 reference statements)

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“…Key miRNAs and target genes have been reported to be mainly related to the PI3K–Akt signaling pathway in GI cancers ( Lai et al, 2019 ). A bioinformatics analysis showed that the DEGs of EC compared with normal tissues are mainly enriched in the PI3K–Akt signaling pathway ( Li M. et al, 2020 ; Yu-Jing et al, 2020 ). Moreover, GLI1 co-expressed and DEGs between tumor samples and normal tissues were both largely enriched in the PI3K–Akt pathway in STAD ( Yu et al, 2018 ; Li et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

m5C RNA Methylation Primarily Affects the ErbB and PI3K–Akt Signaling Pathways in Gastrointestinal Cancer

Xiang

Shen

et al. 2020

Front. Mol. Biosci.

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5-Methylcytosine (m5C) is a kind of methylation modification that occurs in both DNA and RNA and is present in the highly abundant tRNA and rRNA. It has an important impact on various human diseases including cancer. The function of m5C is modulated by regulatory proteins, including methyltransferases (writers) and special binding proteins (readers). This study aims at comprehensive study of the m5C RNA methylation-related genes and the main pathways under m5C RNA methylation in gastrointestinal (GI) cancer. Our result showed that the expression of m5C writers and reader was mostly up-regulated in GI cancer. The NSUN2 gene has the highest proportion of mutations found in GI cancer. Importantly, in liver cancer, higher expression of almost all m5C regulators was significantly associated with lower patient survival rate. In addition, the expression level of m5C-related genes is significantly different at various pathological stages. Finally, we have found through bioinformatics analysis that m5C regulatory proteins are closely related to the ErbB/PI3K–Akt signaling pathway and GSK3B was an important target for m5C regulators. Besides, the compound termed streptozotocin may be a key candidate drug targeting on GSK3B for molecular targeted therapy in GI cancer.

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Section: Discussionmentioning

confidence: 99%

m5C RNA Methylation Primarily Affects the ErbB and PI3K–Akt Signaling Pathways in Gastrointestinal Cancer

Xiang

Shen

et al. 2020

Front. Mol. Biosci.

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“…The GEO database (https://www.ncbi.nlm.nih.gov/geo/) is a publicly available database of gene expression data that stores a large amount of microarray data [12]. Six datasets from the GEO database (GSE23400, GSE20347, GSE29001, GSE53625, GSE45670 and GSE26886) were used to determine PPFIA1 mRNA expression in ESCC and normal tissues.…”

Section: The Geo Databasementioning

confidence: 99%

High expression of PPFIA1 in human esophageal squamous cell carcinoma correlates with tumor progression and poor prognosis

Tang

Jia

Gong

et al. 2022

Preprint

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We aimed to investigate the expression and clinical value of PTPRF interacting protein alpha 1 (PPFIA1) in esophageal squamous cell carcinoma (ESCC). The Oncomine, GEPIA, and GEO databases were utilized to explore PPFIA1 mRNA expression in esophageal cancer. The associations of PPFIA1 expression with clinicopathological variables and prognosis were evaluated in the GSE53625 dataset and verified in qRT-PCR-based cDNA array and immunohistochemistry-based tissue microarray (TMA) datasets. The interactions between PPFIA1 and other genes based on the protein-protein interaction (PPI) network was analyzed via the STRING website. We found PPFIA1 expression was obviously upregulated in ESCC tissues versus adjacent normal tissues according to online database analyses (P<0.05). High PPFIA1 expression was significantly associated with several clinicopathological features, including tumor size, histological grade, tumor invasion depth, lymph node metastasis, and TNM stage. High PPFIA1 expression was related to worse outcomes and was identified as an independent prognostic indicator of overall survival in ESCC patients (GSE53625 dataset, P=0.004; cDNA array dataset, P<0.001; TMA dataset, P=0.039). PPI analysis demonstrated that PPFIA1 was highly correlated with multiple genes, including UNC13B, RAB3A, PTPRD, and SYT1. In conclusion, PPFIA1 may be associated with ESCC progression and could be used as a biomarker for prognostic evaluation in ESCC patients.

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“…The GEO database is a publicly available database of gene expression data that stores a large amount of microarray data (https://www.ncbi.nlm.nih.gov/geo/) [11]. Six datasets from the GEO database (GSE23400, GSE20347, GSE29001, GSE53625, GSE45670 and GSE26886) were used to determine PPFIA1 mRNA expression in ESCC and normal tissues.…”

Section: The Geo Databasementioning

confidence: 99%

High Expression of PPFIA1 Is Associated With Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma

Zhang

Jia

Yang

et al. 2021

Preprint

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Background: PTPRF interacting protein alpha 1 (PPFIA1) is reportedly related to the occurrence and progression of several types of malignancies. However, its role in esophageal squamous cell carcinoma (ESCC) remains unknown. We aimed to investigate the expression and clinical value of PPFIA1 in ESCC.Methods: The Oncomine, Gene Expression Profiling Enrichment Analysis (GEPIA), and Gene Expression Omnibus (GEO) databases were utilized to explore PPFIA1 mRNA expression in esophageal cancer. The associations of PPFIA1 expression with clinicopathological variables and prognosis were evaluated in the GSE53625 dataset and verified in quantitative real-time polymerase chain reaction (qRT-PCR)-based cDNA array and immunohistochemistry (IHC)-based tissue microarray (TMA) datasets. The interactions between PPFIA1 and other genes based on the protein-protein interaction (PPI) network was analyzed via the STRING website.Results: PPFIA1 expression was obviously upregulated in ESCC tissues versus adjacent normal tissues according to online database analyses (all P<0.05). High PPFIA1 expression was significantly associated with several clinicopathological features, including tumor size, histological grade, tumor invasion depth, lymph node metastasis, and tumor-node-metastasis (TNM) stage. High PPFIA1 expression was related to worse outcomes and was identified as an independent prognostic indicator of overall survival (OS) in ESCC patients GSE53625 dataset, P=0.004; cDNA array dataset, P<0.001; TMA dataset, P=0.039). PPI analysis demonstrated that PPFIA1 was highly correlated with multiple genes, including UNC13B, RAB3A, PTPRD, and SYT1.Conclusion: PPFIA1 may be associated with ESCC progression and could be used as a biomarker for prognostic evaluation in ESCC patients.

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Integrated Analysis of Hub Genes and Pathways In Esophageal Carcinoma Based on NCBI’s Gene Expression Omnibus (GEO) Database: A Bioinformatics Analysis

Cited by 8 publications

References 60 publications

m5C RNA Methylation Primarily Affects the ErbB and PI3K–Akt Signaling Pathways in Gastrointestinal Cancer

m5C RNA Methylation Primarily Affects the ErbB and PI3K–Akt Signaling Pathways in Gastrointestinal Cancer

High expression of PPFIA1 in human esophageal squamous cell carcinoma correlates with tumor progression and poor prognosis

High Expression of PPFIA1 Is Associated With Tumor Progression and a Poor Prognosis in Esophageal Squamous Cell Carcinoma

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