Investigation of the miRNA and mRNA Coexpression Network and Their Prognostic Value in Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33274225", "kind": "science-record", "revision": 7, "content_hash": "sha256:37fca41a9c03263538dfa052cbfc1247c6f020fc917295ee2b9cce76c1193b53", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T22:02:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of the miRNA and mRNA Coexpression Network and Their Prognostic Value in Hepatocellular Carcinoma.", "doi": "10.1155/2020/8726567", "pmid": "33274225", "authors": ["Hao Zhang", "Xi Chen", "Yufeng Yuan"], "journal": "BioMed research international", "year": 2020, "abstract": "PURPOSE: To identify pivotal differentially expressed miRNAs and genes and construct their regulatory network in hepatocellular carcinoma.\nMETHODS: mRNA (GSE101728) and microRNA (GSE108724) microarray datasets were obtained from the NCBI Gene Expression Omnibus (GEO) database. Then, we identified the differentially expressed miRNAs and mRNAs. Sequentially, transcription factor enrichment and gene ontology (GO) enrichment analysis for miRNA were performed. Target genes of these differential miRNAs were obtained using packages in R language (R package multiMiR). After that, downregulated miRNAs were matched with target mRNAs which were upregulated, while upregulated miRNAs were paired with downregulated target mRNA using scripts written in Perl. An miRNA-mRNA network was constructed and visualized in Cytoscape software. For miRNAs in the network, survival analysis was performed. And for genes in the network, we did gene ontology (GO) and KEGG pathway enrichment analysis.\nRESULTS: A total of 35 miRNAs and 295 mRNAs were involved in the network. These differential genes were enriched in positive regulation of cell-cell adhesion, positive regulation of leukocyte cell-cell adhesion, and so on. Eight differentially expressed miRNAs were found to be associated with the OS of patients with HCC. Among which, miR-425 and miR-324 were upregulated while the other six, including miR-99a, miR-100, miR-125b, miR-145, miR-150, and miR-338, were downregulated.\nCONCLUSION: In conclusion, these results can provide a potential research direction for further studies about the mechanisms of how miRNA affects malignant behavior in hepatocellular carcinoma.", "claims": [{"id": "claim-method", "statement": "The related clinical data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database. A total of 368 HCC patients with complete available miRNA expression and follow-up datasets were involved in the overall survival analysis. Patients were divided into two groups according to the median value of the expression of miRNA that we want to study (high vs. low expression). Kaplan-Meier survival analysis was performed, and P value of 5-year survival rates was calculated and displayed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33274225", "locator": "sections[8] \"2.6. Overall Survival (OS) Analysis of the miRNAs\" paragraph 2", "quote": "The related clinical data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database. A total of 368 HCC patients with complete available miRNA expression and follow-up datasets were involved in the overall survival analysis. Patients were divided into two groups according to the median value of the expression of miRNA that we want to study (high vs. low expression). Kaplan-Meier survival analysis was performed, and P value of 5-year survival rates was calculated and displayed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33274225", "locator": "sections[13] \"Data Availability\" paragraph 2", "quote": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/)."}], "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:33274225"], "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:GSE101728"], "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:GSE101728"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33274225", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/8726567", "sha256": "sha256:bdd7c4781c0209e139dc37cf66aa0f0f0206c40d954ecdbbf430ca66f77a696a", "bytes": 27377, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/8726567", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7676931", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101728", "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=GSE101728", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101728", "version": null, "note": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2714128", "GSM2714129", "GSM2714130", "GSM2714131", "GSM2714132", "GSM2714133", "GSM2714134", "GSM2714135", "GSM2714136", "GSM2714137", "GSM2714138", "GSM2714139", "GSM2714140", "GSM2714141"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "21047", "taxon": "Homo sapiens", "title": "Expression profiling of lncRNA and mRNA in Hepatocellular carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE108724", "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=GSE108724", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108724", "version": null, "note": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2912551", "GSM2912552", "GSM2912553", "GSM2912554", "GSM2912555", "GSM2912556", "GSM2912557", "GSM2912558", "GSM2912559", "GSM2912560", "GSM2912561", "GSM2912562", "GSM2912563", "GSM2912564"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "20712", "taxon": "Homo sapiens", "title": "Microarray profiling of miRNA in Hepatocellular carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE101728 not downloaded", "asset:data:geo:GSE101728 licence not read", "asset:data:geo:GSE108724 not downloaded", "asset:data:geo:GSE108724 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The related clinical data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database. A total of 368 HCC patients with complete available miRNA expression and follow-up datasets were involved in the overall survival analysis. Patients were divided into two groups according to the median value of the expression of miRNA that we want to study (high vs. low expression). Kaplan-Meier survival analysis was performed, and P value of 5-year survival rates was calculated and displayed."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE101728", "GSE108724"], "resolved_accessions": ["GSE101728", "GSE108724"], "statements": ["The mRNA (GSE101728) and microRNA (GSE108724) microarray datasets during the current study are available in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE101728, GSE108724 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:33274225", "data:geo:GSE101728"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101728"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 20180, "completion_tokens": 1489, "cached_tokens": 528}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33274225", "type": "paper", "label": "pmid:33274225"}, {"id": "source:pmid:33274225", "type": "manuscript", "label": "PMID 33274225 full text"}, {"id": "data:geo:GSE101728", "type": "dataset", "label": "GEO GSE101728"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33274225", "type": "paper", "label": "pmid:33274225"}, {"id": "source:pmid:33274225", "type": "manuscript", "label": "PMID 33274225 full text"}, {"id": "data:geo:GSE101728", "type": "dataset", "label": "GEO GSE101728"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33274225", "type": "extraction", "used": ["source:pmid:33274225"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101728", "type": "accession_resolution", "used": ["data:geo:GSE101728"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33274225", "parent_hash": "sha256:03c6ab394be42f360022a092b9f4c37a50e644c6842b772a7965551a1e63149a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE101728 licence not read", "asset:data:geo:GSE101728 not downloaded", "asset:data:geo:GSE108724 licence not read", "asset:data:geo:GSE108724 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The related clinical data of HCC patients were downloaded from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database. A total of 368 HCC patients with complete available miRNA expression and follow-up datasets were involved in the overall survival analysis. Patients were divided into two groups according to the median value of the expression of miRNA that we want to study (high vs. low expression). Kaplan-Meier survival analysis was performed, and P value of 5-year survival rates was calculated and displayed."], "order_basis": "analysis_only", "id": "assay:1"}]}