Identification of the hub genes in gastric cancer through weighted gene co-expression network analysis

Background Gastric cancer is one of the most lethal tumors and is characterized by poor prognosis and lack of effective diagnostic or therapeutic biomarkers. The aim of this study was to find hub genes serving as biomarkers in gastric cancer diagnosis and therapy. Methods GSE66229 from Gene Expression Omnibus (GEO) was used as training set. Genes bearing the top 25% standard deviations among all the samples in training set were performed to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, hub genes were further screened by using the “least absolute shrinkage and selection operator” (LASSO) logistic regression. Finally, hub genes were validated in the GSE54129 dataset from GEO by supervised learning method artificial neural network (ANN) algorithm. Results Twelve modules with strong preservation were identified by using WGCNA methods in training set. Of which, five modules significantly related to gastric cancer were selected as clinically significant modules, and 713 candidate genes were identified from these five modules. Then, ADIPOQ, ARHGAP39, ATAD3A, C1orf95, CWH43, GRIK3, INHBA, RDH12, SCNN1G, SIGLEC11 and LYVE1 were screened as the hub genes. These hub genes successfully differentiated the tumor samples from the healthy tissues in an independent testing set through artificial neural network algorithm with the area under the receiver operating characteristic curve at 0.946. Conclusions These hub genes bearing diagnostic and therapeutic values, and our results may provide a novel prospect for the diagnosis and treatment of gastric cancer in the future.

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Identification and Validation of the Hub Genes in Gastric Cancer Through Weighted Gene Co-Expression Network Analysis

10.21203/rs.3.rs-34166/v1 ◽

2020 ◽

Author(s):

Chunyang Li ◽

Haopeng Yu ◽

Yajing Sun ◽

Xiaoxi Zeng ◽

Wei Zhang

Keyword(s):

Gastric Cancer ◽

Logistic Regression ◽

Network Analysis ◽

Candidate Genes ◽

Characteristic Curve ◽

Gene Expression Omnibus ◽

Training Set ◽

Hub Genes ◽

Clinically Significant ◽

Logistic Regression Algorithm

Abstract Background: Gastric cancer is one of the most lethal tumors and is characterized by poor prognosis and lack of effective diagnostic or therapeutic biomarkers. The aim of this study was to find hub genes serving as biomarkers in gastric cancer diagnosis and therapy. Methods: GSE66229 from Gene Expression Omnibus (GEO) was used as training set. Genes bearing the top 25% standard deviations among all the samples in training set were performed to systematic weighted gene co-expression network analysis (WGCNA) to find candidate genes. Then, hub genes were further screened by using the “least absolute shrinkage and selection operator” (LASSO) logistic regression. Finally, hub genes were validated in GS54129 dataset from GEO by supervised learning methods logistic regression algorithms.Results: 12 modules with strong preservation were identified by using WGCNA methods in training set. Of which, two modules significantly related to gastric cancer were selected as clinically significant modules, and 43 candidate genes were identified from these two modules. Then, ACADL, ADIPOQ, ARHGAP39, ATAD3A, C1orf95, CCKBR, GRIK3, SCNN1G, SIGLEC11, and TXLNB were screened as the hub genes. These hub genes successfully differentiated the tumor samples from the healthy tissues in an independent testing set through the logistic regression algorithm, with the area under the receiver operating characteristic curve at 0.882. Conclusions: These hub genes bearing diagnostic and therapeutic values, and our results may provide a novel prospect for the diagnosis and treatment of gastric cancer in the future.

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