Identification of hub genes and pathways in hepatitis B virus-associated hepatocellular carcinoma: A comprehensive in silico study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38895552", "kind": "science-record", "revision": 3, "content_hash": "sha256:777e410929d34d19d632100cc69059a365304697cc54056efba4bc1ac2245592", "created_at": "2026-11-01T20:28:58Z", "updated_at": "2026-11-01T22:12:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and pathways in hepatitis B virus-associated hepatocellular carcinoma: A comprehensive in silico study.", "doi": "10.1002/hsr2.2185", "pmid": "38895552", "authors": ["Niloufar Sadat Kalaki", "Mozhgan Ahmadzadeh", "Atena Mansouri", "Mohammadreza Saberiyan", "Mohammad Hadi Karbalaie Niya"], "journal": "Health science reports", "year": 2024, "abstract": "Background and Aim: The hepatitis B virus (HBV) is one of the most common causes of liver cancer in the world. This study aims to provide a better understanding of the mechanisms involved in the development and progression of HBV-associated hepatocellular carcinoma (HCC) by identifying hub genes and the pathways related to their functions.\nMethods: GSE83148 and GSE94660 were selected from the Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) with an adjusted p-value < 0.05 and a |logFC| ≥1 were identified. Common DEGs of two data sets were identified using the GEO2R tool. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) databases were used to identify pathways. Protein-protein interactions (PPIs) analysis was performed by using the Cytoscap and Gephi. A Gene Expression Profiling Interactive Analysis (GEPIA) analysis was carried out to confirm the target genes.\nResults: One hundred and ninety-eight common DEGs and 49 hub genes have been identified through the use of GEO and PPI, respectively. The GO and KEGG pathways analysis showed DEGs were enriched in the G1/S transition of cell cycle mitotic, cell cycle, spindle, and extracellular matrix structural constituent. The expression of four genes (TOP2A, CDK1, CCNA2, and CCNB2) with high scores in module 1 were more in tumor samples and have been identified by GEPIA analysis.\nConclusion: In this study, the hub genes and their related pathways involved in the development of HBV-associated HCC were identified. These genes, as potential diagnostic biomarkers, may provide a potent opportunity to detect HBV-associated HCC at the earliest stages, resulting in a more effective treatment.", "claims": [{"id": "claim-method", "statement": "Using the GEO2R online tool, we obtained 927 and 2114 DEGs from GSE83148 and GSE94660, respectively, adjusted p value < 0.05 and |log FC| ≥1 as the cutoff criteria to identify DEGs, then, we applied Venn diagram software to detect the common DEGs among the two data sets (Figure 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38895552", "locator": "sections[10] \"Common DEGs in HCC patients\" paragraph 2", "quote": "Using the GEO2R online tool, we obtained 927 and 2114 DEGs from GSE83148 and GSE94660, respectively, adjusted p value < 0.05 and |log FC| ≥1 as the cutoff criteria to identify DEGs, then, we applied Venn diagram software to detect the common DEGs among the two data sets (Figure 1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38895552", "locator": "sections[25] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "One hundred and ninety‐eight common DEGs and 49 hub genes have been identified through the use of GEO and PPI, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38895552", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "One hundred and ninety‐eight common DEGs and 49 hub genes have been identified through the use of GEO and PPI, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "One hundred and ninety‐eight common DEGs and 49 hub genes have been identified through the use of GEO and PPI, respectively.", "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:38895552"], "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:GSE83148"], "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:GSE83148"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38895552", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/hsr2.2185", "sha256": "sha256:4998ff6a7de9a297414d02556709ab5ed371cec3f2c5f3592b9d4421e468d68a", "bytes": 45462, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/hsr2.2185", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11183944", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE83148", "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=GSE83148", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE83148", "version": null, "note": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2195416", "GSM2195417", "GSM2195418", "GSM2195419", "GSM2195420", "GSM2195421", "GSM2195422", "GSM2195423", "GSM2195424", "GSM2195425", "GSM2195426", "GSM2195427", "GSM2195428", "GSM2195429", "GSM2195430", "GSM2195431", "GSM2195432", "GSM2195433", "GSM2195434", "GSM2195435", "GSM2195436", "GSM2195437", "GSM2195438", "GSM2195439", "GSM2195440", "GSM2195441", "GSM2195442", "GSM2195443", "GSM2195444", "GSM2195445", "GSM2195446", "GSM2195447", "GSM2195448", "GSM2195449", "GSM2195450", "GSM2195451", "GSM2195452", "GSM2195453", "GSM2195454", "GSM2195455", "GSM2195456", "GSM2195457", "GSM2195458", "GSM2195459", "GSM2195460", "GSM2195461", "GSM2195462", "GSM2195463", "GSM2195464", "GSM2195465", "GSM2195466", "GSM2195467", "GSM2195468", "GSM2195469", "GSM2195470", "GSM2195471", "GSM2195472", "GSM2195473", "GSM2195474", "GSM2195475", "GSM2195476", "GSM2195477", "GSM2195478", "GSM2195479", "GSM2195480", "GSM2195481", "GSM2195482", "GSM2195483", "GSM2195484", "GSM2195485", "GSM2195486", "GSM2195487", "GSM2195488", "GSM2195489", "GSM2195490", "GSM2195491", "GSM2195492", "GSM2195493", "GSM2195494", "GSM2195495", "GSM2195496", "GSM2195497", "GSM2195498", "GSM2195499", "GSM2195500", "GSM2195501", "GSM2195502", "GSM2195503", "GSM2195504", "GSM2195505", "GSM2195506", "GSM2195507", "GSM2195508", "GSM2195509", "GSM2195510", "GSM2195511", "GSM2195512", "GSM2195513", "GSM2195514", "GSM2195515", "GSM2195516", "GSM2195517", "GSM2195518", "GSM2195519", "GSM2195520", "GSM2195521", "GSM2195522", "GSM2195523", "GSM2195524", "GSM2195525", "GSM2195526", "GSM2195527", "GSM2195528", "GSM2195529", "GSM2195530", "GSM2195531", "GSM2195532", "GSM2195533", "GSM2195534", "GSM2195535", "GSM2195536", "GSM2195537", "GSM2291960", "GSM2291961", "GSM2291962", "GSM2291963", "GSM2291964", "GSM2291965"], "sample_count": 128, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data of HBV infected liver tissue", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE94660", "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=GSE94660", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE94660", "version": null, "note": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2480436", "GSM2480437", "GSM2480438", "GSM2480439", "GSM2480440", "GSM2480441", "GSM2480442", "GSM2480443", "GSM2480444", "GSM2480445", "GSM2480446", "GSM2480447", "GSM2480448", "GSM2480449", "GSM2480450", "GSM2480451", "GSM2480452", "GSM2480453", "GSM2480454", "GSM2480455", "GSM2480456", "GSM2480457", "GSM2480458", "GSM2480459", "GSM2480460", "GSM2480461", "GSM2480462", "GSM2480463", "GSM2480464", "GSM2480465", "GSM2480466", "GSM2480467", "GSM2480468", "GSM2480469", "GSM2480470", "GSM2480471", "GSM2480472", "GSM2480473", "GSM2480474", "GSM2480475", "GSM2480476", "GSM2480477"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "RNA sequencing (RNA-SEQ) of 21 HBV-HCC patients with non-neoplastic liver and tumor tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE83148 not downloaded", "asset:data:geo:GSE83148 licence not read", "asset:data:geo:GSE94660 not downloaded", "asset:data:geo:GSE94660 licence not read"]}, "analysis": {"state": "partial", "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": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential expression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the GEO2R online tool, we obtained 927 and 2114 DEGs from GSE83148 and GSE94660, respectively, adjusted p value < 0.05 and |log FC| ≥1 as the cutoff criteria to identify DEGs, then, we applied Venn diagram software to detect the common DEGs among the two data sets (Figure 1)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE83148", "GSE94660"], "resolved_accessions": ["GSE83148", "GSE94660"], "statements": ["The authors confirm that the data supporting the findings of this study are available within the article [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] its supplementary materials. [Dr. Mohammadreza Saberiyan and Dr. Mohammad Hadi Karbalaie Niya] had full access to all of the data in this study and take complete responsibility for the integrity of the data and the accuracy of the data analysis."], "basis": "The paper names GSE83148, GSE94660 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:38895552", "data:geo:GSE83148"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE83148"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:21:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12457, "completion_tokens": 1473, "cached_tokens": 128}}, "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:38895552", "type": "paper", "label": "pmid:38895552"}, {"id": "source:pmid:38895552", "type": "manuscript", "label": "PMID 38895552 full text"}, {"id": "data:geo:GSE83148", "type": "dataset", "label": "GEO GSE83148"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38895552", "type": "paper", "label": "pmid:38895552"}, {"id": "source:pmid:38895552", "type": "manuscript", "label": "PMID 38895552 full text"}, {"id": "data:geo:GSE83148", "type": "dataset", "label": "GEO GSE83148"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38895552", "type": "extraction", "used": ["source:pmid:38895552"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE83148", "type": "accession_resolution", "used": ["data:geo:GSE83148"], "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:38895552", "parent_hash": "sha256:89d71006b21d78799d4512e5ac51f9fdcee6131a0fa30d9d34f0739d436b7191", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE83148 licence not read", "asset:data:geo:GSE83148 not downloaded", "asset:data:geo:GSE94660 licence not read", "asset:data:geo:GSE94660 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["PPI"], "order_basis": "analysis_only", "id": "assay:1"}]}