Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31275757", "kind": "science-record", "revision": 7, "content_hash": "sha256:9957cfa6823071bb6fd4bd75d33a8c712f5e0d50ed717c806f8e9135bbc7c673", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T22:00:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples.", "doi": "10.7717/peerj.7171", "pmid": "31275757", "authors": ["Huimei Wang", "Mingwei Zhang", "Qiqi Xie", "Jin Yu", "Yan Qi", "Qiuyuan Yue"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Major depressive disorder (MDD) is a severe disease characterized by multiple pathological changes. However, there are no reliable diagnostic biomarkers for MDD. The aim of the current study was to investigate the gene network and biomarkers underlying the pathophysiology of MDD.\nMETHODS: In this study, we conducted a comprehensive analysis of the mRNA expression profile of MDD using data from Gene Expression Omnibus (GEO). The MDD dataset (GSE98793) with 128 MDD and 64 control whole blood samples was divided randomly into two non-overlapping groups for cross-validated differential gene expression analysis. The gene ontology (GO) enrichment and gene set enrichment analysis (GSEA) were performed for annotation, visualization, and integrated discovery. Protein-protein interaction (PPI) network was constructed by STRING database and hub genes were identified by the CytoHubba plugin. The gene expression difference and the functional similarity of hub genes were investigated for further gene expression and function exploration. Moreover, the receiver operating characteristic curve was performed to verify the diagnostic value of the hub genes.\nRESULTS: We identified 761 differentially expressed genes closely related to MDD. The Venn diagram and GO analyses indicated that changes in MDD are mainly enriched in ribonucleoprotein complex biogenesis, antigen receptor-mediated signaling pathway, catalytic activity (acting on RNA), structural constituent of ribosome, mitochondrial matrix, and mitochondrial protein complex. The GSEA suggested that tumor necrosis factor signaling pathway, Toll-like receptor signaling pathway, apoptosis pathway, and NF-kappa B signaling pathway are all crucial in the development of MDD. A total of 20 hub genes were selected via the PPI network. Additionally, the identified hub genes were downregulated and show high functional similarity and diagnostic value in MDD.\nCONCLUSIONS: Our findings may provide novel insight into the functional characteristics of MDD through integrative analysis of GEO data, and suggest potential biomarkers and therapeutic targets for MDD.", "claims": [{"id": "claim-method", "statement": "Functional and pathway enrichment were analyzed using hypergeometric test and Bonferroni correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31275757", "locator": "sections[5] \"Functional and pathway enrichment analysis\" paragraph 2", "quote": "Functional and pathway enrichment were analyzed using hypergeometric test and Bonferroni correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files as Tables S1 and S2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31275757", "locator": "sections[32] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files as Tables S1 and S2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31275757"], "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:GSE98793"], "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:GSE98793"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31275757", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.7171", "sha256": 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