Identification of novel biomarkers linking depressive disorder and Alzheimer's disease based on an integrative bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37061663", "kind": "science-record", "revision": 4, "content_hash": "sha256:314cf651f2c65285674cbfa946f570e60adad31a2f04df98f917ca2f664d9c7b", "created_at": "2026-11-01T19:01:43Z", "updated_at": "2026-11-01T22:51:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of novel biomarkers linking depressive disorder and Alzheimer's disease based on an integrative bioinformatics analysis.", "doi": "10.1186/s12863-023-01120-x", "pmid": "37061663", "authors": ["Jin Song", "Zilong Ma", "Huishi Zhang", "Ting Liang", "Jun Zhang"], "journal": "BMC genomic data", "year": 2023, "abstract": "BACKGROUND: Previous reports revealed that a history of major depressive disorder (MDD) increased the risk of Alzheimer's disease (AD). The immune disorder is associated with MDD and AD pathophysiology. We aimed to identify differentially expressed immune-related genes (DEIRGs) that are involved in the pathogenesis of MDD and AD.\nMETHODS: We downloaded mRNA expression profiles (GSE76826 and GSE5281) from the Gene Expression Omnibus (GEO) database. The R software was used to identify DEIRGs for the two diseases separately. Functional enrichment analysis and PPI network of DEIRGs were performed. Finally, the relationship between shared DEIRGs and immune infiltrates of AD and MDD were analyzed, respectively.\nRESULTS: A total of 121 DEIRGs linking AD and MDD were identified. These genes were significantly enriched in immune-related pathways, such as the JAK-STAT signaling pathway, regulation of chemotaxis, chemotaxis, cytokine-cytokine receptor interaction, and primary immunodeficiency. Furthermore, three shared DEIRGs (IL1R1, CHGB, and NRG1) were identified. Correlation analysis between DEIRGs and immune cells revealed that IL1R1 and NRG1 had a negative or positive correlation with some immune cells both in AD and MDD.\nCONCLUSION: Both DEIRGs and immune cell infiltrations play a vital role in the pathogenesis of AD and MDD. Our findings indicated that there are common genes and biological processes between MDD and AD, which provides a theoretical basis for the study of the comorbidity of MDD and AD.", "claims": [{"id": "claim-method", "statement": "First, the “limma” package of R software was used to identify differentially expressed genes in GSE76826 and GSE5281 datasets based on p < 0.05 and ∣logFC∣ ≥ 0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37061663", "locator": "sections[4] \"Identification of differentially expressed IRGs (DEIRGs) in AD and MDD\" paragraph 2", "quote": "First, the “limma” package of R software was used to identify differentially expressed genes in GSE76826 and GSE5281 datasets based on p < 0.05 and ∣logFC∣ ≥ 0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the present study are available in the GEO database: GSE76826 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE76826); GSE5281 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE5281); GSE98793 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE98793); GSE132903 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE132903).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37061663", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed during the present study are available in the GEO database: GSE76826 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE76826); GSE5281 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE5281); GSE98793 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE98793); GSE132903 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE132903)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 121 DEIRGs linking AD and MDD were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37061663", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 121 DEIRGs linking AD and MDD were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 121 DEIRGs linking AD and MDD were identified.", "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:37061663"], "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:GSE132903"], "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:GSE132903"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37061663", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12863-023-01120-x", "sha256": 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"identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE132903 not downloaded", "asset:data:geo:GSE132903 licence not read", "asset:data:geo:GSE5281 not downloaded", "asset:data:geo:GSE5281 licence not read", "asset:data:geo:GSE76826 not downloaded", "asset:data:geo:GSE76826 licence not read", "asset:data:geo:GSE98793 not downloaded", "asset:data:geo:GSE98793 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "First, the “limma” package of R software was used to identify differentially expressed genes in GSE76826 and GSE5281 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"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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE76826", "GSE5281", "GSE98793", "GSE132903"], "resolved_accessions": ["GSE76826", "GSE5281", "GSE98793", "GSE132903"], "statements": ["The datasets analyzed during the present study are available in the GEO database: GSE76826 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE76826); GSE5281 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE5281); GSE98793 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE98793); GSE132903 (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE132903)."], "basis": "The paper names GSE76826, GSE5281, GSE98793, GSE132903 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:37061663", "data:geo:GSE132903"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE132903"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:36:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12087, "completion_tokens": 1678, "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:37061663", "type": "paper", "label": "pmid:37061663"}, {"id": "source:pmid:37061663", "type": "manuscript", "label": "PMID 37061663 full text"}, {"id": "data:geo:GSE132903", "type": "dataset", "label": "GEO GSE132903"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37061663", "type": "paper", "label": "pmid:37061663"}, {"id": "source:pmid:37061663", "type": "manuscript", "label": "PMID 37061663 full text"}, {"id": "data:geo:GSE132903", "type": "dataset", "label": "GEO GSE132903"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37061663", "type": "extraction", "used": ["source:pmid:37061663"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE132903", "type": "accession_resolution", "used": ["data:geo:GSE132903"], "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:37061663", "parent_hash": "sha256:37f7383df31175762413331496be07af00cfc2fae8c425d4ddd9d610b43036f9", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE132903 licence not read", "asset:data:geo:GSE132903 not downloaded", "asset:data:geo:GSE5281 licence not read", "asset:data:geo:GSE5281 not downloaded", "asset:data:geo:GSE76826 licence not read", "asset:data:geo:GSE76826 not downloaded", "asset:data:geo:GSE98793 licence not read", "asset:data:geo:GSE98793 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["First, the “limma” package of R software was used to identify differentially expressed genes in GSE76826 and GSE5281 datasets based on p < 0.05 and ∣logFC∣ ≥ 0.5."], "order_basis": "analysis_only", "id": "assay:1"}]}