Screening Hub Genes of Hepatocellular Carcinoma Based on Public Databases

Abstract

Tumor recurrence and metastasis often occur in HCC patients after surgery, and the prognosis is not optimistic. Hence, searching effective biomarkers for prognosis of is of great importance. Firstly, HCC-related data was acquired from the TCGA and GEO databases. Based on GEO data, 256 differentially expressed genes (DEGs) were obtained firstly. Subsequently, to clarify function of DEGs, clusterProfiler package was used to conduct functional enrichment analyses on DEGs. Protein-protein interaction (PPI) network analysis screened 20 key genes. The key genes were filtered via GEPIA database, by which 11 hub genes (F9, CYP3A4, ASPM, AURKA, CDC20, CDCA5, NCAP, PRC1, PTTG1, TOP2A, and KIFC1) were screened out. Then, univariate Cox analysis was applied to construct a prognostic model, followed by a prediction performance validation. With the risk score calculated by the model and common clinical features, univariate and multivariate analyses were carried out to assess whether the prognostic model could be used independently for prognostic prediction. In conclusion, the current study screened HCC prognostic gene signature based on public databases.

Pan-cancer analysis reveals tumor microbiome associations with host molecular aberrations

“…LIHC patients had an overabundance of Orthohepadnavirus (HBV genus), which is a major causative etiological factor. Overall, 13 consistent hub genes identified by our work and recent studies [15][16][17] were confirmed to be associated with HBV infection (Figure S1A, Table S1). Our gene set overrepresentation analysis using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that genes associated with the HBV genus were enriched in biological pathways like mitotic nuclear division, cell cycle, DNA replication, chromosome segregation and nuclear division, which were also consistent with previously identified pathways that may contribute to the pathogenesis of HBV-infected liver cancer (Figure S1A) 17 .…”

The clinical significance of integrin subunit alpha V in cancers: from small cell lung carcinoma to pan-cancer

“…A gene with a absolute value of log 2 (fold change) ≥ 1 through the limma package [17][18][19] and SMD < 0 was identified as having low-expression genes (LEGs) in SCLC. A gene that was positively related to ITGAV expression (Pearson coefficient ≥ 0.3, p < 0.05) in > 30% (4/12) datasets was considered as ITGAV-positivelyrelated genes (ITGAV-PRGs).…”

Identification of prognostic biomarkers for suppressing tumorigenesis and metastasis of Hepatocellular carcinoma through transcriptome analysis

“…KIF2C resulted in tumorigenesis due to abnormal cell cycle progression and metastasis in cervical cancer (Yang et al, 2022). In case of HCC, it participated in the progression of HCC and could be a potential therapeutic target (Gao et al, 2021). On the other hand, in case of GBM, it had missense mutations at three different locations on phosphorylation, ubiquitination, acetylation, and methylation PTM sites with diploid and gain copy number alterations.…”

“…Cancer is a complex disease caused due to uncontrolled division and growth of cells, categorized according to the progression in organs such as breast cancer, blood cancer, colon cancer, liver cancer, etc. Liver cancer, also known as hepatocellular carcinoma (HCC), has nowadays become a common cancer type, with approximately 830000 deaths in 2020 alone ( Gao et al, 2021). Tumorigenesis or transformation of normal cells into cancerous cells often results in uncontrolled cell proliferation, metastasis, and apoptosis evasion (Cao, 2017).…”