Bioinformatics screening of biomarkers related to liver cancer

Ye-Cheng Wang,Xu-Qing Tang,Zhen-Bo Tian

doi:10.1186/s12859-021-04411-1

Ye-Cheng Wang, Xu-Qing Tang + Show 1 more

Open Access

https://doi.org/10.1186/s12859-021-04411-1

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Abstract

BackgroundLiver cancer is a common malignant tumor in China, with high mortality. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abundant data on gene expression, mRNA quantification and the clinical data of liver cancer. However, the hub genes, which can be served as biomarkers for diagnosis and treatment of early liver cancer, are not well screened.ResultsHere we present a new method for getting 6 key genes, aiming to diagnose and treat the early liver cancer. We firstly analyzed the different expression microarrays based on TCGA database, and a total of 1564 differentially expressed genes were obtained, of which 1400 were up-regulated and 164 were down-regulated. Furthermore, these differentially expressed genes were studied by using GO and KEGG enrichment analysis, a PPI network was constructed based on the STRING database, and 15 hub genes were obtained. Finally, 15 hub genes were verified by applying the survival analysis method on Oncomine database, and 6 key genes were ultimately identified, including PLK1, CDC20, CCNB2, BUB1, MAD2L1 and CCNA2. The robustness analysis of four independent data sets verifies the accuracy of the key gene’s classification of the data set.ConclusionsAlthough there are complicated differences between cancer and normal cells in gene functions, cancer cells could be differentiated in case that a group of special genes expresses abnormally. Here we presented a new method to identify the 6 key genes for diagnosis and treatment of early liver cancer, and these key genes can help us understand the pathogenesis of liver cancer more deeply.

Highlights

Liver cancer is a common malignant tumor in China, with high mortal‐ ity
1564 Differentially expressed genes (DEG) were enriched by Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) with The database for annotation (DAVID), where β = 0.01 was included as inclusion criteria in GO, and p value < 0.05 was included as inclusion criteria in KEGG
Import the data downloaded in the STRING database into Cytoscape software for visualization, and get the protein-protein interaction (PPI) network diagram of DEGs

Summary

Introduction

Liver cancer is a common malignant tumor in China, with high mortal‐ ity. The hub genes, which can be served as biomarkers for diagnosis and treatment of early liver cancer, are not well screened. Detection and treatment can effectively improve the prognosis of tumor patients and reduce the mortality rate, but there are usually no obvious clinical symptoms in the early stage of liver cancer. The commonly used diagnostic methods of liver cancer, such as serological tumor markers and imaging techniques, are not satisfactory in clinical effect. Screening markers related to early diagnosis, invasion and metastasis of liver cancer is of great significance for improving the therapeutic effect and prognosis of liver cancer [5]

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