Diagnostic significance and potential function of miR-338-5p in hepatocellular carcinoma: A bioinformatics study with microarray and RNA sequencing data

Abstract

MicroRNA (miR)-338-5p has been studied in hepatocellular carcinoma (HCC); however, the diagnostic value and molecular mechanism underlying its actions remains to be elucidated. The present study aimed to validate the diagnostic ability of miR-338-5p and further explore the underlying molecular mechanism. Data from eligible studies, Gene Expression Omnibus (GEO) chips and The Cancer Genome Atlas (TCGA) datasets were gathered in the data mining and the integrated meta-analysis, to evaluate the significance of miR-338-5p in diagnosing HCC comprehensively. The potential target genes of miR-338-5p were achieved from the intersection of the deregulated targets of miR-338-5p from GEO and TCGA in addition to the predicted target genes from 12 online software. A protein-protein-interaction (PPI) network was drawn to illustrate the interaction between target genes and to define the hub genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to investigate the function of the target genes. From the results, miR-338-5p exhibited favorable value in diagnosing HCC. Types of sample and experiment were defined as the possible sources of heterogeneity in meta-analysis. A total of 423 genes were selected as the potential target genes of miR-338-5p, and five genes were defined as the hub genes from the PPI network. The GO and KEGG analyses indicated that the target genes were significantly assembled in the pathways of metabolic process and cell cycle. miR-338-5p may function as a novel diagnostic target for HCC through regulating certain target genes and signaling pathways.

Identification of the potential therapeutic target gene UBE2C in human hepatocellular carcinoma: An investigation based on GEO and TCGA databases

“…The GEO database is a public database of microarray profile founded by the National Center for Biotechnology Information and provides access to high-throughput screening of abnormally expressed genes in cancerous tissues (7). Numerous studies have explored microarray data profiling (8,9). However, although reliable molecular biomarkers have been clinically observed in patients with HCC, the underlying molecular mechanisms of HCC remain to be clarified.…”

Stabilization of miRNAs in esophageal cancer contributes to radioresistance and limits efficacy of therapy

“…miR-338-5p is located on chromosome 17q25.3 and often originates from an intron of the gene encoding the apoptosis-associated tyrosine kinase (AATK) [84]. It has been reported to be correlated with the carcinogenesis and progression of several human cancers, including colon [85], glioma [86], glioblastoma [87], hepatocellular [88] and esophageal squamous cell carcinoma [19].…”

Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach

“…Samples were collected from airway tissue during bronchoscopies and total RNA was extracted from these. Patients were divided in three categories: those diagnosed with lung cancer (97), those not diagnosed with lung cancer (90) and those suspected to be under cancer development (5). Although based on a relatively old platform (the Affymetrix U133A array), this dataset in particular was chosen for its suitability to specifically study the underlying genetic impairment in lung carcinoma in smoker patients.…”

“…Therefore, not only are GNs able to identify genes related to biological processes, but also the relationships among these genes, thus providing a comprehensive picture of the studied processes [3]. GNs have been widely applied in various fields such as biology, biomedicine or bioinformatics [4,5] among others.…”