Identification and RT-qPCR Validation of Biomarkers Based on Butyrate Metabolism-Related Genes to Predict Recurrent Miscarriage.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39372587", "kind": "science-record", "revision": 3, "content_hash": "sha256:ce000f15f9750eb6526c581438e4d14e6ef32b76be49413dafae809b0a94d449", "created_at": "2026-11-01T20:29:35Z", "updated_at": "2026-11-01T22:12:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and RT-qPCR Validation of Biomarkers Based on Butyrate Metabolism-Related Genes to Predict Recurrent Miscarriage.", "doi": "10.2147/JIR.S470087", "pmid": "39372587", "authors": ["Wei Wang", "Haobo Chen", "Qiaochu Zhou"], "journal": "Journal of inflammation research", "year": 2024, "abstract": "Purpose: To date, the cause of recurrent miscarriage (RM) in at least 50% of patients remains unknown. However, no study has explored the correlation between butyrate metabolism-related genes (BMRGs) and RM.\nMethods: RM-related datasets (GSE165004, GSE111974, GSE73025, and GSE179996) were obtained from the Gene Expression Omnibus (GEO) database. First, 595 differentially expressed genes (DEGs) were identified between the RM and control samples in GSE165004. Subsequently, 213 differentially expressed BMRGs (DE-BMRGs) were identified by considering the intersection of DEGs with BMRGs. The protein-protein interaction (PPI)network of DE-BMRGs contained 156 nodes and 250 edges, and a key module was obtained. In total, four biomarkers (ACTR2, ANXA2, PFN1, and OAS1) were acquired through least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and random forest (RF). Immune analysis revealed two immune cells and three immune-related gene sets that were significantly different between the RM and control groups, namely, T helper cells, regulatory T cells (Treg), MHC class I, parainflammation, and type I IFN response. In addition, a TF-mRNA network based on the top 100 nodes ranked in the order of connectivity was created, including 100 nodes and 253 edges, such as MTERF2-ACTR2, NKX23-PFN1, STAT1-OAS1, and SP100-ANXA2.\nResults: Finally, 3 drugs (withaferin A, N-ethylmaleimide, and etoposide) were predicted to interact with 2 biomarkers (ANXA2 and ACTR2). Eventually, ANXA2 and OAS1 were significantly downregulated, and PFN1 was markedly overexpressed in the RM group, as determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR).\nConclusion: Our findings authenticated four butyrate metabolism-related biomarkers for the diagnosis of RM, providing a scientific reference for further studies on RM treatment.", "claims": [{"id": "claim-method", "statement": "Differences between the groups were analyzed using the Wilcoxon test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39372587", "locator": "sections[13] \"Statistical Analysis\" paragraph 2", "quote": "Differences between the groups were analyzed using the Wilcoxon test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39372587", "locator": "sections[27] \"Data Sharing Statement\" paragraph 2", "quote": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ANXA2 and OAS1 were significantly downregulated, and PFN1 was markedly overexpressed in the RM group, as determined by RT-qPCR.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39372587", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eventually, ANXA2 and OAS1 were significantly downregulated, and PFN1 was markedly overexpressed in the RM group, as determined by reverse transcription quantitative polymerase chain reaction (RT-qPCR)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "ANXA2 and OAS1 were significantly downregulated, and PFN1 was markedly overexpressed in the RM group, as determined by RT-qPCR.", "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:39372587"], "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:GSE111974"], "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:group_comparison_wilcoxon", "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:GSE111974"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39372587", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S470087", "sha256": "sha256:8256943137ececf19888df98966f76e7632eaf207c3c18c5df0fcb48c696bc2d", "bytes": 41254, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S470087", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11453136", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE111974", "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=GSE111974", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE111974", "version": null, "note": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3045867", "GSM3045868", "GSM3045869", "GSM3045870", "GSM3045871", "GSM3045872", "GSM3045873", "GSM3045874", "GSM3045875", "GSM3045876", "GSM3045877", "GSM3045878", "GSM3045879", "GSM3045880", "GSM3045881", "GSM3045882", "GSM3045883", "GSM3045884", "GSM3045885", "GSM3045886", "GSM3045887", "GSM3045888", "GSM3045889", "GSM3045890", "GSM3045891", "GSM3045892", "GSM3045893", "GSM3045894", "GSM3045895", "GSM3045896", "GSM3045897", "GSM3045898", "GSM3045899", "GSM3045900", "GSM3045901", "GSM3045902", "GSM3045903", "GSM3045904", "GSM3045905", "GSM3045906", "GSM3045907", "GSM3045908", "GSM3045909", "GSM3045910", "GSM3045911", "GSM3045912", "GSM3045913", "GSM3045914"], "sample_count": 48, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Endometrial Tissue RNA expression in Recurrent Implantation Failure vs. Conrol", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE165004", "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=GSE165004", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE165004", "version": null, "note": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5024320", "GSM5024321", "GSM5024322", "GSM5024323", "GSM5024324", "GSM5024325", "GSM5024326", "GSM5024327", "GSM5024328", "GSM5024329", "GSM5024330", "GSM5024331", "GSM5024332", "GSM5024333", "GSM5024334", "GSM5024335", "GSM5024336", "GSM5024337", "GSM5024338", "GSM5024339", "GSM5024340", "GSM5024341", "GSM5024342", "GSM5024343", "GSM5024344", "GSM5024345", "GSM5024346", "GSM5024347", "GSM5024348", "GSM5024349", "GSM5024350", "GSM5024351", "GSM5024352", "GSM5024353", "GSM5024354", "GSM5024355", "GSM5024356", "GSM5024357", "GSM5024358", "GSM5024359", "GSM5024360", "GSM5024361", "GSM5024362", "GSM5024363", "GSM5024364", "GSM5024365", "GSM5024366", "GSM5024367", "GSM5024368", "GSM5024369", "GSM5024370", "GSM5024371", "GSM5024372", "GSM5024373", "GSM5024374", "GSM5024375", "GSM5024376", "GSM5024377", "GSM5024378", "GSM5024379", "GSM5024380", "GSM5024381", "GSM5024382", "GSM5024383", "GSM5024384", "GSM5024385", "GSM5024386", "GSM5024387", "GSM5024388", "GSM5024389", "GSM5024390", "GSM5024391"], "sample_count": 72, "group_sizes": null, "group_sizes_basis": null, "platform": "16699", "taxon": "Homo sapiens", "title": "Endometrial Tissue RNA expression in recurrent pregnancy losses and unexplained infertility vs. conrol", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE179996", "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=GSE179996", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE179996", "version": null, "note": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5444660", "GSM5444661", "GSM5444662", "GSM5444663", "GSM5444664", "GSM5444665", "GSM5444666", "GSM5444667", "GSM5444668", "GSM5444669"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "21827", "taxon": "Homo sapiens", "title": "Long Noncoding RNA RP11-115N4.1Promotes Inflammatory Responses by Interacting with HNRNPH3 and Enhancing the Transcription of HSP70 in Unexplained Recurrent Spontaneous Abortion", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE73025", "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=GSE73025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73025", "version": null, "note": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1880973", "GSM1880974", "GSM1880975", "GSM1880976", "GSM1880977", "GSM1880978", "GSM1880979", "GSM1880980", "GSM1880981", "GSM1880982"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "20917", "taxon": "Human alphaherpesvirus 1; Cytomegalovirus; Betapolyomavirus macacae; Human immunodeficiency virus 1; Human alphaherpesvirus 2; Lymphocryptovirus; JC polyomavirus; Betapolyomavirus hominis; Homo sapiens; Rhadinovirus; Merkel cell polyomavirus", "title": "Expression profile of micro-RNAs and functional annotation analysis of their targets in human chorionic villi from early recurrent miscarriage", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE111974 not downloaded", "asset:data:geo:GSE111974 licence not read", "asset:data:geo:GSE165004 not downloaded", "asset:data:geo:GSE165004 licence not read", "asset:data:geo:GSE179996 not downloaded", "asset:data:geo:GSE179996 licence not read", "asset:data:geo:GSE73025 not downloaded", "asset:data:geo:GSE73025 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differences between the groups were analyzed using the Wilcoxon test."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}, {"id": "method-4", "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"}}, {"id": "method-5", "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": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE165004", "GSE111974", "GSE73025", "GSE179996"], "resolved_accessions": ["GSE165004", "GSE111974", "GSE73025", "GSE179996"], "statements": ["The raw data used in this study for analysis and validation are available from GEO: GSE165004, GSE111974, GSE73025, and GSE179996."], "basis": "The paper names GSE165004, GSE111974, GSE73025, GSE179996 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:39372587", "data:geo:GSE111974"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE111974"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:34:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11337, "completion_tokens": 1927, "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:39372587", "type": "paper", "label": "pmid:39372587"}, {"id": "source:pmid:39372587", "type": "manuscript", "label": "PMID 39372587 full text"}, {"id": "data:geo:GSE111974", "type": "dataset", "label": "GEO GSE111974"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39372587", "type": "paper", "label": "pmid:39372587"}, {"id": "source:pmid:39372587", "type": "manuscript", "label": "PMID 39372587 full text"}, {"id": "data:geo:GSE111974", "type": "dataset", "label": "GEO GSE111974"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39372587", "type": "extraction", "used": ["source:pmid:39372587"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE111974", "type": "accession_resolution", "used": ["data:geo:GSE111974"], "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:39372587", "parent_hash": "sha256:e50308d24c794d161b6eb96957f79d1151fc9145e0210995465b50e41d6eb197", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE111974 licence not read", "asset:data:geo:GSE111974 not downloaded", "asset:data:geo:GSE165004 licence not read", "asset:data:geo:GSE165004 not downloaded", "asset:data:geo:GSE179996 licence not read", "asset:data:geo:GSE179996 not downloaded", "asset:data:geo:GSE73025 licence not read", "asset:data:geo:GSE73025 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "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": ["Identification and RT-qPCR Validation of Biomarkers Based on Butyrate M", "tion quantitative polymerase chain reaction (RT-qPCR). Conclusion: Our findings authenticated fou", "n quantitative polymerase chain reaction (RT-qPCR). Conclusion: Our findings authenticated fou"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"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": ["Differences between the groups were analyzed using the Wilcoxon test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}