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Identification of the critical genes and miRNAs in hepatocellular carcinoma by integrated bioinformatics analysis

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Abstract

Hepatocellular carcinoma (HCC) is a global health problem with complex etiology and pathogenesis. Microarray data are increasingly being used as a novel and effective method for cancer pathogenesis analysis. An integrative analysis of genes and miRNA for HCC was conducted to unravel the potential prognosis of HCC. Two gene microarray datasets (GSE89377 and GSE101685) and two miRNA expression profiles (GSE112264 and GSE113740) were obtained from Gene Expression Omnibus database. A total of 177 differently expressed genes (DEGs) and 80 differently expressed miRNAs (DEMs) were screened out. Functional enrichment of DEGs was proceeded by Clue GO and these genes were significantly enriched in the chemical carcinogenesis pathway. A protein–protein interaction network was then established on the STRING platform, and ten hub genes (CDC20, TOP2A, ASPM, NCAPG, AURKA, CYP2E1, HMMR, PRC1, TYMS, and CYP4A11) were visualized via Cytoscape software. Then, a miRNA–target network was established to identify the hub dysregulated miRNA. A key miRNA (hsa-miR-124-3p) was filtered. Finally, the miRNA–target–transcription factor network was constructed for hsa-miR-124-3p. The network for hsa-miR-124-3p included two transcription factors (TFs) and five targets. These identified DEGs and DEMs, TFs, targets, and regulatory networks may help advance our understanding of the underlying pathogenesis of HCC.

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Abbreviations

HCC:

Hepatocellular carcinoma

PLC:

Primary liver cancer

GEO:

Gene Expression Omnibus

TFs:

Transcription factors

PPI:

Protein–protein interaction

DEGs:

Differently expressed genes

DEMs:

Differently expressed miRNAs

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

BP:

Biological process

MF:

Molecular function

CC:

Cellular component

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Acknowledgements

We appreciate the GEO database and contributors providing their platforms and their meaningful datasets.

Funding

This work was supported by the Hefei University Scientific Research and Development Fund (20ZR09ZDB) and the Talent Research Fund Project of Hefei University (20RC48).

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Authors and Affiliations

  1. School of Biological Food and Environment, Hefei University, Hefei, 230601, China

    Jun Wang, Chuyan Wang, Liuqing Yang & Kexin Li

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  1. Jun Wang
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  2. Chuyan Wang
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Correspondence to Jun Wang.

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Wang, J., Wang, C., Yang, L. et al. Identification of the critical genes and miRNAs in hepatocellular carcinoma by integrated bioinformatics analysis. Med Oncol 39, 21 (2022). https://doi.org/10.1007/s12032-021-01622-7

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  • DOI: https://doi.org/10.1007/s12032-021-01622-7

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