Screening and function analysis of hub genes and pathways in hepatocellular carcinoma via bioinformatics approaches.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29843214", "kind": "science-record", "revision": 4, "content_hash": "sha256:f53abcf6e08e02adb0229ff3c03512b8783efb04acda4c1af5d0c83848940e4d", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:59:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening and function analysis of hub genes and pathways in hepatocellular carcinoma via bioinformatics approaches.", "doi": "10.3233/CBM-171160", "pmid": "29843214", "authors": ["Liang Zhang", "Yi Huang", "Junjun Ling", "Wenlei Zhuo", "Zhen Yu", "Mengmeng Shao", "Yunbo Luo", "Yi Zhu"], "journal": "Cancer biomarkers : section A of Disease markers", "year": 2018, "abstract": "BACKGROUND: Liver carcinoma is a major cause of cancer-related death worldwide. Up to date, the mechanisms of liver cancerigenesis and development have not been fully understood. Multi-genes and pathways were involved in the tumorigenesis of liver cancer.\nOBJECTIVE: The aim of the present study was to screen key genes and pathways in liver cancerigenesis and development by using bioinformatics methods.\nMETHODS: A dataset GSE64041 were retrieved from GEO database and the differentially expressed genes (DEGs) were screened out. Then the DEG functions were annotated by gene ontology (GO) and pathway enrichment analysis, respectively. The hub genes were further selected by protein-protein interaction (PPI) analysis. Afterwards, the mRNA and protein expressions as well as the prognostic values of the hub genes were assessed.\nRESULTS: As a result, 208 up-regulated and 82 down-regulated genes were screened out. These DEGs were mainly enriched in cell cycle and metabolism-related pathways. Through PPI analysis, TOP2A, PRDM10, CDK1, AURKA, BUB1, PLK1, CDKN3, NCAPG, BUB1B and CCNA2 were selected as hub genes, which were all over-expressed in liver cancers relative to those in normal tissues, respectively. Among them, PLK1 and CCNA2 were suggested to be prognostic factors for liver carcinoma.\nCONCLUSION: In conclusion, the present study identified several hub genes, and cell cycle and metabolism-related pathways that may play critical roles in the tumorigenesis of liver cancer. Future validation laboratory experiments are required to confirm the results.", "claims": [{"id": "claim-target-result", "statement": "Using GSE64041 retrieved from GEO, the study screened differentially expressed genes, applied GO and pathway enrichment analyses plus PPI analysis, and identified 208 up-regulated and 82 down-regulated genes, with PLK1 and CCNA2 suggested as prognostic factors for liver carcinoma.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29843214", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A dataset GSE64041 were retrieved from GEO database and the differentially expressed genes (DEGs) were screened out."}, {"asset": "source:pmid:29843214", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Then the DEG functions were annotated by gene ontology (GO) and pathway enrichment analysis, respectively."}, {"asset": "source:pmid:29843214", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The hub genes were further selected by protein-protein interaction (PPI) analysis."}, {"asset": "source:pmid:29843214", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "As a result, 208 up-regulated and 82 down-regulated genes were screened out."}, {"asset": "source:pmid:29843214", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Among them, PLK1 and CCNA2 were suggested to be prognostic factors for liver carcinoma."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using GSE64041 retrieved from GEO, the study screened differentially expressed genes, applied GO and pathway enrichment analyses plus PPI analysis, and identified 208 up-regulated and 82 down-regulated genes, with PLK1 and CCNA2 suggested as prognostic factors for liver carcinoma.", "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:29843214"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29843214", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3233/CBM-171160", "sha256": "sha256:02432c86963e49da4c32f85c0a78dbc031e69cb30bd8f6b02f841b441692fe46", "bytes": 1529, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3233/CBM-171160", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC13078479", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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