Comprehensive analysis of key lncRNAs in HCV-positive hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33488867", "kind": "science-record", "revision": 9, "content_hash": "sha256:0b3b628cb35c3a982ea65295ccb986d26707c8f26abc85a8acf38103bf2c5502", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T22:46:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of key lncRNAs in HCV-positive hepatocellular carcinoma.", "doi": "10.5114/aoms.2020.100675", "pmid": "33488867", "authors": ["Jingqi Liu", "Ligang Chen", "Jinshui Pan", "Meiya Chen", "Jingping Zhou", "Fei Zhou", "Peizhong Chen", "Yang Song"], "journal": "Archives of medical science : AMS", "year": 2021, "abstract": "INTRODUCTION: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Despite the therapeutic advances in HCC in the past few decades, the mortality rate of HCC is still high. Hepatitis C (HCV) infection is one of the major etiological risk factors of HCCs. However, the underlying mechanisms of HCV-induced hepatocarcinogenesis remain largely unclear.\nMATERIAL AND METHODS: Our study represented the comprehensive analysis of differentially expressed lncRNAs in HCV-positive HCC for the first time by analyzing the public dataset GSE17856. Co-expression network and gene ontology (GO) analysis revealed the functions of those differentially expressed lncRNAs.\nRESULTS: We identified 256 upregulated lncRNAs and 198 downregulated lncRNAs in HCV- positive HCC compared to the normal liver tissues. Co-expression network and GO analysis showed that these lncRNAs were involved in regulating metabolism, energy pathways, proliferation and the immune response. Seven lncRNAs (LOC341056, CCT6P1, PTTG3P, LOC643387, LOC100133920, C3P1 and C22orf45) were identified as key lncRNAs and co-expressed with more than 100 differentially expressed genes (DEGs) in HCV-related HCC. Kaplan-Meier analysis showed that higher expression levels of LOC643387, PTTG3P, LOC341056, CCT6P1 and lower expression levels of C3P1 and C22orf45 were associated with shorter survival time in the TCGA dataset.\nCONCLUSIONS: We believe that this study can provide novel potential therapeutic and prognostic biomarkers for HCV-positive HCC.", "claims": [{"id": "claim-method", "statement": "A t-test [20] in the limma [21] package, in R [22] was used to identify genes which were differentially expressed between normal and HCV-positive HCC samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33488867", "locator": "sections[5] \"Identification of DElncs\" paragraph 2", "quote": "A t-test [20] in the limma [21] package, in R [22] was used to identify genes which were differentially expressed between normal and HCV-positive HCC samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray data were obtained from the study by Tsuchiya et al. [18], which is referenced in the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under accession number GSE17856. The platform is GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F Array. A total of 44 non-tumoral liver and 43 tumors sample were obtained from 47 subjects with HCV-associated HCC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33488867", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Microarray data were obtained from the study by Tsuchiya et al. [18], which is referenced in the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under accession number GSE17856. The platform is GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F Array. A total of 44 non-tumoral liver and 43 tumors sample were obtained from 47 subjects with HCV-associated HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33488867"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE17856"], "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": ["data:geo:GSE17856"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33488867", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5114/aoms.2020.100675", "sha256": "sha256:b9035e041ce72213d2a10093fd55c6bfd0afb46fbdc5cc4b6069ed3fc5e49915", "bytes": 23276, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5114/aoms.2020.100675", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7811325", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17856", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17856", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17856", "version": null, "note": "Microarray data were obtained from the study by Tsuchiya et al. [18], which is referenced in the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under accession number GSE17856. The platform is GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F Array. A total of 44 non-tumoral liver and 43 tumors sample were obtained from 47 subjects with HCV-associated HCC.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray data were obtained from the study by Tsuchiya et al. [18], which is referenced in the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under accession number GSE17856. The platform is GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F Array. 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