Analysis of potential immune-related genes involved in the pathogenesis of ischemia-reperfusion injury following liver transplantation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37006305", "kind": "science-record", "revision": 4, "content_hash": "sha256:a42772040621d7e8027df807e59388be273de848811bb18f694951cb1d90b26d", "created_at": "2026-11-01T19:01:39Z", "updated_at": "2026-11-01T22:51:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of potential immune-related genes involved in the pathogenesis of ischemia-reperfusion injury following liver transplantation.", "doi": "10.3389/fimmu.2023.1126497", "pmid": "37006305", "authors": ["Jiayu Guo", "Shangting Han", "Qi Chen", "Tianyu Wang", "Bo Yu", "Jiangqiao Zhou", "Tao Qiu"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: Hepatic ischemia-reperfusion (I/R) injury is an unavoidable pathological process that occurs after liver transplantation. However, the immune-related molecular mechanism still remains unclear. This study aims to further explore the biological mechanisms of immune-related genes in hepatic I/R injury.\nMethods: Gene microarray data was downloaded from the Gene Expression Omnibus (GEO) expression profile database and the differentially expressed genes (DEGs) were taken for intersection. After identifying common DEGs, functional annotation, protein-protein interaction (PPI) network, and modular construction were performed. The immune-related hub genes were obtained, which their upstream transcription factors and non-RNAs were predicted. Validation of the hub genes expression and immune infiltration were performed in a mouse model of hepatic I/R injury.\nResults: A total of 71 common DEGs were obtained from three datasets (GSE12720, GSE14951, GSE15480). The GO and KEGG enrichment analysis results indicated that immune and inflammatory response played an important role in hepatic I/R injury. Finally, 9 immune-related hub genes were identified by intersecting cytoHubba with immune-related genes, including SOCS3, JUND, CCL4, NFKBIA, CXCL8, ICAM1, IRF1, TNFAIP3, and JUN.\nConclusion: Our study revealed the importance of the immune and inflammatory response in I/R injury following liver transplantation and provided new insights into the therapeutic of hepatic I/R injury.", "claims": [{"id": "claim-method", "statement": "The three raw datasets were downloaded using the R “GEOquery” package, and then performed gene annotation, gene filtering, normalization, etc. on the three datasets. The differentially expressed genes (DEGs) were analyzed and compared between the pre-ischemic and reperfused liver tissue controls using the R “limma” package. Only those genes with adjusted P-value < 0.05 and |log2FC (fold change)| ≥ 0.5 were considered DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37006305", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "The three raw datasets were downloaded using the R “GEOquery” package, and then performed gene annotation, gene filtering, normalization, etc. on the three datasets. The differentially expressed genes (DEGs) were analyzed and compared between the pre-ischemic and reperfused liver tissue controls using the R “limma” package. Only those genes with adjusted P-value < 0.05 and |log2FC (fold change)| ≥ 0.5 were considered DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: immune-related gene (http://www.immport.org/) and the Gene expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (Accession: GSE12720, GSE14951 and GSE15480).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37006305", "locator": "sections[27] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: immune-related gene (http://www.immport.org/) and the Gene expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (Accession: GSE12720, GSE14951 and GSE15480)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 71 common DEGs were obtained from three datasets (GSE12720, GSE14951, GSE15480).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37006305", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 71 common DEGs were obtained from three datasets (GSE12720, GSE14951, GSE15480)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 71 common DEGs were obtained from three datasets (GSE12720, GSE14951, GSE15480).", "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:37006305"], "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:GSE12720"], "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:GSE12720"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37006305", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1126497", "sha256": "sha256:2822c1aa8764278829861d4592068583e45cc817f2e3e980a5ce8fd7cd609f71", "bytes": 46993, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1126497", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10060527", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12720", "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=GSE12720", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12720", "version": null, "note": "Publicly available datasets were analyzed in this study. 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This data can be found here: immune-related gene (http://www.immport.org/) and the Gene expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (Accession: GSE12720, GSE14951 and GSE15480).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. This data can be found here: immune-related gene (http://www.immport.org/) and the Gene expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (Accession: GSE12720, GSE14951 and GSE15480).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM372247", "GSM372248", "GSM372249", "GSM372250", "GSM372251", "GSM372252", "GSM372254", "GSM372256", "GSM372257", "GSM372567", "GSM372599", "GSM372600", "GSM373314", "GSM373315", "GSM373324"], "sample_count": 15, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": " Gene expression profile in human orthotopic liver transplantation", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE15480", "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=GSE15480", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15480", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: immune-related gene (http://www.immport.org/) and the Gene expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/) (Accession: GSE12720, GSE14951 and GSE15480).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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Methods: Gene microarray data was downloaded from the Gene Expression"], "order_basis": "paper_text_order:418", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["and immune infiltration were performed in a mouse model of hepatic I/R injury. Results: A total of 7", "and immune infiltration were performed in a mouse model of hepatic I/R injury. Results: A tota", "of the Renmin hospital of Wuhan University. Mice were kept in an air-filtered, temperature-control", "d free access to a standard diet. The stable mouse model of partial liver warm ischemia was construct"], "order_basis": "paper_text_order:929", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The three raw datasets were downloaded using the R “GEOquery” package, and then performed gene annotation, gene filtering, normalization, etc. on the three datasets. The differentially expressed genes (DEGs) were analyzed and compared between the pre-ischemic and reperfused liver tissue controls using the R “limma” package. Only those genes with adjusted P-value < 0.05 and |log2FC (fold change)| ≥ 0.5 were considered DEGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}