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

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.

• Publication year

  2017

• Venue

  Molecular Medicine Reports

• Publication date

  2017-11-21

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.3892/mmr.2017.8125PMID 29207053PMCID 5783480
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Functional enrichment analysis linked the target genes to metabolic process and cell cycle.

  Confidence 0.89

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• 423 candidate target genes were selected for miR-338-5p, and five PPI network hub genes were defined.

  Confidence 0.92

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• Sample type and experiment type were identified as possible sources of heterogeneity in the meta-analysis.

  Confidence 0.87

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• miR-338-5p showed favorable diagnostic performance for hepatocellular carcinoma.

  Confidence 0.95

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review

• cell cycle

  pathway

  A pathway or process category used to describe the functional annotation of the candidate target genes.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• functional enrichment analysis

  analysis method

  GO and KEGG-based analysis used to summarize the functions and pathways associated with the candidate target genes.

  Aliases: GO and KEGG enrichment analysis, GO/KEGG analysis

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• hepatocellular carcinoma

  cancer type

  A primary liver cancer used as the disease context for the biomarker analysis.

  Aliases: HCC

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• meta-analysis

  analysis method

  A pooled statistical synthesis of eligible studies and datasets used to evaluate diagnostic performance.

  Aliases: integrated meta-analysis, meta analysis

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• metabolic process

  biological process

  A biological process category used to describe the functional annotation of the candidate target genes.

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• mir-338-5p

  microRNA

  A microRNA examined as a diagnostic biomarker candidate in hepatocellular carcinoma.

  Aliases: microRNA-338-5p

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• ppi network hub genes

  gene set

  The most connected genes identified from the protein-protein interaction network built for the candidate targets.

  Aliases: hub genes, hub genes from the PPI network

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review
• target genes

  gene set

  Candidate downstream genes of miR-338-5p obtained from intersecting deregulated and predicted gene sets.

  Aliases: candidate target genes, predicted target genes

  박진우 (dztg5apj7m) extraction뀨 (7c402c1b98) reviewq (76h6bfydm6) reviewKiller Whale (322360f1c1) reviewB (s683577b42) reviewAK (4715169a40) reviewAnonymous (12632b8b5f) review

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