Identification of differentially expressed genes associated with ferroptosis in Crohn's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38274342", "kind": "science-record", "revision": 3, "content_hash": "sha256:6ee5e52464f25b37a14f96cceaad3d841a5a44c8895f140c404b61443fbf6dae", "created_at": "2026-11-01T19:20:12Z", "updated_at": "2026-11-01T22:11:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of differentially expressed genes associated with ferroptosis in Crohn's disease.", "doi": "10.3892/etm.2024.12378", "pmid": "38274342", "authors": ["Wenquan Zhang", "Zhaoshui Li", "Hongbo Li", "Dianliang Zhang"], "journal": "Experimental and therapeutic medicine", "year": 2024, "abstract": "Ferroptosis-related genes may play a critical regulatory role in the pathogenesis of Crohn's disease (CD). The purpose of the present study was to identify genes expressed in CD that are associated with ferroptosis, and to provide guidance in the diagnosis and therapy of CD. CD mRNA expression data were initially gathered from the Gene Expression Omnibus (GEO) database. GSE75214 and GSE102133 datasets were selected as the major targets and were analyzed for differentially expressed genes (DEGs). Subsequently, R software was used to analyze the common genes among the DEGs between CD and ferroptosis-related genes. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genome pathway analysis were conducted to identify related pathways and functions. Protein-protein interaction (PPI) analysis was performed to identify target genes. The DSigDB website was used to predict potential target drugs for hub genes. Reverse transcription-quantitative (RT-q) PCR was employed to detect the expression of these ferroptosis-related genes in clinical samples obtained from healthy controls and patients with CD. According to the two GEO datasets, 13 ferroptosis DEGs (11 upregulated genes and two downregulated genes) were identified in CD with thresholds of P<0.05 and |log2 fold change|>1, and were selected for further analysis. PPI analysis indicated the mutual effects among these genes and filtered out five hub genes. The top 10 potential targeted drugs were selected. The qPCR results showed that the expression levels of three genes, namely, IL-6, prostaglandin-endoperoxide synthase 2 (PTGS2) and dual oxidase 2 (DUOX2), were different between CD samples and healthy samples. This result was consistent with the results obtained from the bioinformatics analysis. In conclusion, bioinformatics analysis identified a total of 13 ferroptosis-associated genes in CD. Further verification by qPCR showed that IL-6, PTGS2 and DUOX2 may affect the process of CD by regulating ferroptosis. These findings might provide new biomarkers, diagnostic and therapeutic markers for CD.", "claims": [{"id": "claim-method", "statement": "In the qPCR experiment, the results were analyzed by unpaired Student's t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38274342", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "In the qPCR experiment, the results were analyzed by unpaired Student's t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38274342", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of the two GEO datasets identified 13 ferroptosis-related differentially expressed genes in Crohn's disease.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "According to the two GEO datasets, 13 ferroptosis DEGs (11 upregulated genes and two downregulated genes) were identified in CD with thresholds of P<0.05 and |log2 fold change|>1, and were selected for further analysis."}, "evidence": [{"asset": "source:pmid:38274342", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "According to the two GEO datasets, 13 ferroptosis DEGs (11 upregulated genes and two downregulated genes) were identified in CD with thresholds of P<0.05 and |log2 fold change|>1, and were selected for further analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Analysis of the two GEO datasets identified 13 ferroptosis-related differentially expressed genes in Crohn's disease.", "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:38274342"], "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:GSE102133"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE102133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38274342", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/etm.2024.12378", "sha256": "sha256:90e884a77e2cf2b6732890d77906c82a6acdb3d0b9b3a7124996019465a62b9e", "bytes": 35339, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/etm.2024.12378", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10809353", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102133", "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=GSE102133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102133", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2728650", "GSM2728651", "GSM2728652", "GSM2728653", "GSM2728654", "GSM2728655", "GSM2728656", "GSM2728657", "GSM2728658", "GSM2728659", "GSM2728660", "GSM2728661", "GSM2728662", "GSM2728663", "GSM2728664", "GSM2728665", "GSM2728666", "GSM2728667", "GSM2728668", "GSM2728669", "GSM2728670", "GSM2728671", "GSM2728672", "GSM2728673", "GSM2728674", "GSM2728675", "GSM2728676", "GSM2728677", "GSM2728678", "GSM2728679", "GSM2728680", "GSM2728681", "GSM2728682", "GSM2728683", "GSM2728684", "GSM2728685", "GSM2728686", "GSM2728687", "GSM2728688", "GSM2728689", "GSM2728690", "GSM2728691", "GSM2728692", "GSM2728693", "GSM2728694", "GSM2728695", "GSM2728696", "GSM2728697", "GSM2728698", "GSM2728699", "GSM2728700", "GSM2728701", "GSM2728702", "GSM2728703", "GSM2728704", "GSM2728705", "GSM2728706", "GSM2728707", "GSM2728708", "GSM2728709", "GSM2728710", "GSM2728711", "GSM2728712", "GSM2728713", "GSM2728714", "GSM2728715", "GSM2728716", "GSM2728717", "GSM2728718", "GSM2728719", "GSM2728720", "GSM2728721", "GSM2728722", "GSM2728723", "GSM2728724", "GSM2728725", "GSM2728726"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in ileum of patients with Crohn's disease", "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:GSE75214", "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=GSE75214", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE75214", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1426071", "GSM1426072", "GSM1426073", "GSM1426074", "GSM1426075", "GSM1426076", "GSM1426077", "GSM1426078", "GSM1426079", "GSM1426080", "GSM1426081", "GSM1426082", "GSM1426083", "GSM1426084", "GSM1426085", "GSM1426086", "GSM1426087", "GSM1426088", "GSM1426089", "GSM1426090", "GSM1426091", "GSM1426092", "GSM1426093", "GSM1426094", "GSM1426095", "GSM1426096", "GSM1426097", "GSM1426098", "GSM1426099", "GSM1426100", "GSM1426101", "GSM1426102", "GSM1426103", "GSM1426104", "GSM1426105", "GSM1426106", "GSM1426107", "GSM1426108", "GSM1426109", "GSM1426110", "GSM1426111", "GSM1426112", "GSM1426113", "GSM1426114", "GSM1426115", "GSM1426116", "GSM1426117", "GSM1426118", "GSM1426119", "GSM1426120", "GSM1426121", "GSM1426122", "GSM1426123", "GSM1426124", "GSM1426125", "GSM1426126", "GSM1426127", "GSM1426128", "GSM1426129", "GSM1426130", "GSM1426131", "GSM1426132", "GSM1426133", "GSM1426134", "GSM1426135", "GSM1426136", "GSM1426137", "GSM1426138", "GSM1426139", "GSM1426140", "GSM1426141", "GSM1426142", "GSM1426143", "GSM1426144", "GSM1426145", "GSM1426146", "GSM1426147", "GSM1426148", "GSM1426149", "GSM1426150", "GSM1426151", "GSM1426152", "GSM1426153", "GSM1426154", "GSM1426155", "GSM1426156", "GSM1426157", "GSM1426158", "GSM1426159", "GSM1426160", "GSM1426161", "GSM1426162", "GSM1426163", "GSM1426164", "GSM1426165", "GSM1426166", "GSM1426167", "GSM1426168", "GSM1426169", "GSM1426170", "GSM1426171", "GSM1426172", "GSM1426173", "GSM1426174", "GSM1426175", "GSM1426176", "GSM1426177", "GSM1426178", "GSM1426179", "GSM1426180", "GSM1426181", "GSM1426182", "GSM1426183", "GSM1426184", "GSM1426185", "GSM1426186", "GSM1945759", "GSM1945760", "GSM1945761", "GSM1945762", "GSM1945763", "GSM1945764", "GSM1945765", "GSM1945766", "GSM1945767", "GSM1945768", "GSM1945769", "GSM1945770", "GSM1945771", "GSM1945772", "GSM1945773", "GSM1945774", "GSM1945775", "GSM1945776", "GSM1945777", "GSM1945778", "GSM1945779", "GSM1945780", "GSM1945781", "GSM1945782", "GSM1945783", "GSM1945784", "GSM1945785", "GSM1945786", "GSM1945787", "GSM1945788", "GSM1945789", "GSM1945790", "GSM1945791", "GSM1945792", "GSM1945793", "GSM1945794", "GSM1945795", "GSM1945796", "GSM1945797", "GSM1945798", "GSM1945799", "GSM1945800", "GSM1945801", "GSM1945802", "GSM1945803", "GSM1945804", "GSM1945805", "GSM1945806", "GSM1945807", "GSM1945808", "GSM1945809", "GSM1945810", "GSM1945811", "GSM1945812", "GSM1945813", "GSM1945814", "GSM1945815", "GSM1945816", "GSM1945817", "GSM1945818", "GSM1945819", "GSM1945820", "GSM1945821", "GSM1945822", "GSM1945823", "GSM1945824", "GSM1945825", "GSM1945826", "GSM1945827", "GSM1945828", "GSM1945829", "GSM1945830", "GSM1945831", "GSM1945832", "GSM1945833", "GSM1945834", "GSM1945835", "GSM1945836"], "sample_count": 194, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in patients with inflammatory bowel disease study", "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:GSE102133 not downloaded", "asset:data:geo:GSE102133 licence not read", "asset:data:geo:GSE75214 not downloaded", "asset:data:geo:GSE75214 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In the qPCR experiment, the results were analyzed by unpaired Student's t-test."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "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"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE102133", "GSE75214"], "resolved_accessions": ["GSE102133", "GSE75214"], "statements": ["The datasets generated and/or analyzed during the current study are available in the GEO repository, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214. Other datasets used and/or analyzed during the current study are available from the corresponding authors on reasonable request."], "basis": "The paper names GSE102133, GSE75214 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": [], "assets": ["source:pmid:38274342", "data:geo:GSE102133"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102133"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:06:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9857, "completion_tokens": 1323, "cached_tokens": 264}}, "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:38274342", "type": "paper", "label": "pmid:38274342"}, {"id": "source:pmid:38274342", "type": "manuscript", "label": "PMID 38274342 full text"}, {"id": "data:geo:GSE102133", "type": "dataset", "label": "GEO GSE102133"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38274342", "type": "paper", "label": "pmid:38274342"}, {"id": "source:pmid:38274342", "type": "manuscript", "label": "PMID 38274342 full text"}, {"id": "data:geo:GSE102133", "type": "dataset", "label": "GEO GSE102133"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38274342", "type": "extraction", "used": ["source:pmid:38274342"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102133", "type": "accession_resolution", "used": ["data:geo:GSE102133"], "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:38274342", "parent_hash": "sha256:d0b4f7cdcf2adf1c7041c73780f86ce626561c4afca59d5018017c063abf9131", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE102133 licence not read", "asset:data:geo:GSE102133 not downloaded", "asset:data:geo:GSE75214 licence not read", "asset:data:geo:GSE75214 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["potential targeted drugs were selected. The qPCR results showed that the expression levels of", "ociated genes in CD. Further verification by qPCR showed that IL-6, PTGS2 and DUOX2 may affect", "l Hospital (Qingdao, China) in October 2022. RT-qPCR was completed in October 2022, and western b", "the five hub genes in CD clinical samples by RT-qPCR All collected clinical tissue samples of CD"], "order_basis": "paper_text_order:1546", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": [". RT-qPCR was completed in October 2022, and western blotting was completed in November 2023 (approval no.", "alyzed by unpaired Student's t-test. For the western blot experiment, the results were analyzed by unp", "was conducted in normal and CD tissues using western blotting (Fig. 8A and B). The protein expression leve"], "order_basis": "paper_text_order:2990", "id": "assay:2"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["genes associated with ferroptosis in CD The microarray expression profiling datasets GSE102133 and"], "order_basis": "paper_text_order:3564", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In the qPCR experiment, the results were analyzed by unpaired Student's t-test."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}