The online version of this article (https://doi.org/10.1186/s12935-018-0629-5) contains supplementary material, which is available to authorized users.
Guorun Fan and Yaqin Tu contributed equally to this work
Aberrant methylation of DNA is a key driver of hepatocellular carcinoma (HCC). In this study, we sought to integrate four cohorts profile datasets to identify such abnormally methylated genes and pathways associated with HCC.
To this end, we downloaded microarray datasets examining gene expression (GSE84402, GSE46408) and gene methylation (GSE73003, GSE57956) from the GEO database. Abnormally methylated differentially expressed genes (DEGs) were sorted and pathways were analyzed. The String database was then used to perform enrichment and functional analysis of identified pathways and genes. Cytoscape software was used to create a protein–protein interaction network, and MCODE was used for module analysis. Finally, overall survival analysis of hub genes was performed by the OncoLnc online tool.
In total, we identified 19 hypomethylated highly expressed genes and 14 hypermethylated lowly expressed genes at the screening step, and finally found six mostly changed hub genes including MAD2L1, CDC20, CCNB1, CCND1, AR and ESR1. Pathway analysis showed that aberrantly methylated-DEGs mainly associated with the cell cycle process, p53 signaling, and MAPK signaling in HCC. After validation in TCGA database, the methylation and expression status of hub genes was significantly altered and same with our results. Patients with high expression of MAD2L1, CDC20 and CCNB1 and low expression of CCND1, AR, and ESR1 was associated with shorter overall survival.
Taken together, we have identified novel aberrantly methylated genes and pathways linked to HCC, potentially offering novel insights into the molecular mechanisms governing HCC progression and serving as novel biomarkers for precision diagnosis and disease treatment.
Additional file 1: Figure S1. Validation of the expression of hub genes in UALCAN database. Red: Hypomethylation/high-expression genes; Green: Hypermethylation/low-expression genes.
Additional file 2: Figure S2. Validation of the hypermethylation/low-expression hub genes in TCGA database. For the hypermethylation/low-expression hub genes, normal samples tended to have higher expression than tumor samples.
Additional file 3: Figure S3. Validation of the hypomethylation/high-expression hub genes in TCGA database. Tumor samples tended to have higher expression than normal samples for hypomethylation/high-expression hub genes.
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