Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29228631", "kind": "science-record", "revision": 7, "content_hash": "sha256:925379813c2d81354816164530344b94522225a2cd2237d52630a45cc889b678", "created_at": "2026-11-01T15:40:30Z", "updated_at": "2026-11-01T21:21:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients.", "doi": "10.18632/oncotarget.22181", "pmid": "29228631", "authors": ["Sida Liu", "Fujing Xie", "Xiaohong Xiang", "Sinan Liu", "Shunbin Dong", "Kai Qu", "Ting Lin"], "journal": "Oncotarget", "year": 2017, "abstract": "Hepatoblastoma (HB) is one of the most common hepatic malignancies in the pediatric population. HB are composed of a variety of tumors, which derived from different origins and had varying clinical outcomes. However, the unclear underlying mechanisms of HB limited exploring novel biomarkers and effective therapeutic targets. We searched microarray datasets on Gene Expression Omnibus (GEO) database and selected GSE75271 and GSE75283 datasets for comprehensive analysis. Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage. Coexpression analysis of identified genes was also performed and lncRNA-miRNA-mRNA network was finally conducted. Our results showed that a total of 22 lncRNAs, 13 miRNAs and 66 mRNAs were identified to be associated with tumor malignant phenotypes. Mechanistically, these molecules might promote the malignant phenotypes via regulating metabolic pathways. Among of them, 6 miRNAs (hsa-miR-106b, hsa-miR-130b, hsa-miR-19a, hsa-miR-19b, hsa-miR-20a and hsa-miR-301a), 8 lncRNAs (NR_102317, XR_245338, XR_428373, XR_924945, XR_929728, XR_931611, XR_935074 and XR_946696), and 6 mRNAs (EGFR, GAREM, INSIG1, KRT81, SAR1B and SDC1) were selected to conduct a lncRNA-miRNA-mRNA network. Taken together, our findings provide evidence for exploring molecular mechanisms of HB. Those identified malignant phenotype-associated molecules might be potential biomarkers and anti-cancer therapeutic targets in future.", "claims": [{"id": "claim-method", "statement": "For the pair of molecule i and j, Pearson correlation coefficient was computed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29228631", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "For the pair of molecule i and j, Pearson correlation coefficient was computed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. All raw data were downloaded from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29228631", "locator": "sections[9] \"Microarray data\" paragraph 2", "quote": "We finally selected two datasets for bioinformatic analysis, including GSE75271 (mRNA profiling data based on Affymetrix Human Genome U133 Plus 2.0 Array platform) and GSE75283 (miRNA profiling data based on Agilent-029297 Human miRNA Microarray v15 platform), which were derived from the same 50 HB patients and 5 controls [22]. 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Weighted gene correlation network analysis (WGCNA) was employed to identify genes which were associated with tumor malignant phenotypes, including HB subtypes, Cairo classification and tumor stage."}, {"asset": "source:pmid:29228631", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results showed that a total of 22 lncRNAs, 13 miRNAs and 66 mRNAs were identified to be associated with tumor malignant phenotypes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used weighted gene correlation network analysis (WGCNA) on GEO microarray datasets GSE75271 and GSE75283 and identified 22 lncRNAs, 13 miRNAs, and 66 mRNAs associated with HB subtypes, Cairo classification, and tumor stage.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29228631"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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