Weighted Gene Coexpression Network Analysis Identifies Specific Modules and Hub Genes Related to Major Depression.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32214815", "kind": "science-record", "revision": 8, "content_hash": "sha256:fd790293c8d8c53fef99b221070460bd84f0f044ccf2e9fa4a93bd3b1d8a9cef", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T22:44:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Weighted Gene Coexpression Network Analysis Identifies Specific Modules and Hub Genes Related to Major Depression.", "doi": "10.2147/NDT.S244452", "pmid": "32214815", "authors": ["Guangyin Zhang", "Shixin Xu", "Zhuo Yuan", "Li Shen"], "journal": "Neuropsychiatric disease and treatment", "year": 2020, "abstract": "PURPOSE: Despite advances in characterizing the neurobiology of emotional disorders, there is still a significant lack of scientific understanding of the pathophysiological mechanisms governing major depressive disorder (MDD). This study attempted to elucidate the molecular circuitry of MDD and to identify more potential genes associated with the pathogenesis of the disease.\nPATIENTS AND METHODS: Microarray data from the GSE98793 dataset were downloaded from the NCBI Gene Expression Omnibus (GEO) database, including 128 patients with MDD and 64 healthy controls. Weighted gene coexpression network analysis (WGCNA) was performed to find modules of differentially expressed genes (DEGs) with high correlations followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to obtain further biological insight into the top three key modules. The protein-protein interaction (PPI) network, the modules from the PPI network, and the gene annotation enrichment of modules were analyzed, as well.\nRESULTS: We filtered 3276 genes that were considered significant DEGs for further WGCNA analysis. By performing WGCNA, we found that the turquoise, blue and brown functional modules were all strongly correlated with MDD development, including immune response, neutrophil degranulation, ribosome biogenesis, T cell activation, glycosaminoglycan biosynthetic process, and protein serine/threonine kinase activator activity. Hub genes were identified in the key functional modules that might have a role in the progression of MDD. Functional annotation showed that these modules primarily enriched such KEGG pathways as the TNF signaling pathway, T cell receptor signaling pathway, primary immunodeficiency, Th1, Th2 and Th17 cell differentiation, autophagy and RNA degradation and oxidative phosphorylation. These results suggest that these genes are closely related to autophagy and cellular immune function.\nCONCLUSION: The results of this study may help to elucidate the pathophysiology of MDD development at the molecular level and explore the potential molecular mechanisms for new interventional strategies.", "claims": [{"id": "claim-method", "statement": "To characterize DEGs, the control group and the MDD group were analyzed using the LIMMA (linear models for microarray data) package20 in the R/Bioconductor platform.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32214815", "locator": "sections[4] \"Data Preprocessing and DEG Screening\" paragraph 3", "quote": "To characterize DEGs, the control group and the MDD group were analyzed using the LIMMA (linear models for microarray data) package20 in the R/Bioconductor platform."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All of the data were freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32214815", "locator": "sections[3] \"Microarray Data\" paragraph 2", "quote": "All of the data were freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors."}], "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:32214815"], "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:32214815", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/NDT.S244452", "sha256": 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authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All of the data were freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2612096", "GSM2612097", "GSM2612098", "GSM2612099", "GSM2612100", "GSM2612101", "GSM2612102", "GSM2612103", "GSM2612104", "GSM2612105", "GSM2612106", "GSM2612107", "GSM2612108", "GSM2612109", "GSM2612110", "GSM2612111", "GSM2612112", "GSM2612113", "GSM2612114", "GSM2612115", "GSM2612116", "GSM2612117", "GSM2612118", "GSM2612119", "GSM2612120", "GSM2612121", "GSM2612122", "GSM2612123", "GSM2612124", "GSM2612125", "GSM2612126", "GSM2612127", "GSM2612128", "GSM2612129", "GSM2612130", "GSM2612131", "GSM2612132", "GSM2612133", "GSM2612134", "GSM2612135", "GSM2612136", "GSM2612137", "GSM2612138", "GSM2612139", "GSM2612140", "GSM2612141", "GSM2612142", 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"GSM2612285", "GSM2612286", "GSM2612287"], "sample_count": 192, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis in whole blood samples obtained from donors diagnosed with MDD compared to healthy controls", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32214815:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1ad982c58a1eeed8e8d5a57093ccaabe3529452141902d260c11be27c400617c", "bytes": 671, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T0001", "version": null, "note": "Most Significant GO Terms of the Turquoise Module", "structure": {"pmcid": "PMC7079285", "section_index": 13, "section_title": "PPI Network Construction and Analysis of Selected Modules", "row_count": 6, "column_count": 5}, "table": {"label": "Table 1", "caption": "Most Significant GO Terms of the Turquoise Module", "rows": [["GO ID", "P-value", "No. of Genes", "Description", "Hub Gene"], ["GO:0043312", "1.93E-11", "40", "Neutrophil degranulation", "RETN, CAMP, CTSD, MMP9"], ["GO:0002283", "2.49E-11", "40", "Neutrophil activation involved in immune response", "RETN, CAMP, CTSD, MMP9"], ["GO:0002446", "3.21E-11", "40", "Neutrophil mediated immunity", "CAMP, CTSD, MMP9"], ["GO:0035580", "3.61E-09", "13", "Specific granule lumen", "CAMP, CTSD"], ["GO:0034774", "6.63E-09", "28", "secretory granule lumen", "CAMP, CTSD"]], "row_count": 6, "column_count": 5, "numeric_cells": 15, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:32214815:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:89e251231a5af8b8b1022a511b0162c024f6e085209b30b4313a1290dcbc25a6", "bytes": 818, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#T0002", "version": null, "note": "Most Significant GO Terms of the Blue Module", "structure": {"pmcid": "PMC7079285", "section_index": 13, "section_title": "PPI Network Construction and Analysis of Selected Modules", "row_count": 6, "column_count": 5}, "table": {"label": "Table 2", "caption": "Most Significant GO Terms of the Blue Module", "rows": [["GO ID", "P-value", "No. of Genes", "Description", "Hub Gene"], ["GO:0003723", "9.81E-08", "52", "RNA binding", "FBL, RPL11, RPS18, NOP56, RPS5, RPS14, MRTO4, RPL18A, RPL35"], ["GO:0042254", "4.63E-07", "17", "Ribosome biogenesis", "FBL, RPL11, RPS18, NOP56, RPS5, RPS14, MRTO4, RPL18A, RPL35"], ["GO:0016072", "2.30E-06", "15", "rRNA metabolic process", "FBL, RPL11, RPS18, NOP56, RPS5, RPS14, MRTO4, RPL18A, RPL35"], ["GO:0034470", "2.37E-06", "16", "ncRNA processing", "FBL, RPL11, RPS18, NOP56, RPS5, RPS14, MRTO4, RPL18A, RPL35"], ["GO:0006364", "2.60E-06", "15", "rRNA processing", "FBL, RPL11, RPS18, NOP56, RPS5, RPS14, MRTO4, RPL18A, RPL35"]], "row_count": 6, "column_count": 5, "numeric_cells": 20, "header_rows": 1, "locator": "section[13]/table-wrap[2]#T0002"}}, {"id": "asset:table:pmid:32214815:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:63b08b7b9129f71281bac85441aadb4e7ebab56474b3708083e78da15ca946f2", "bytes": 617, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[3]#T0003", "version": null, "note": "Most Significant GO Terms of the Brown Module", "structure": {"pmcid": "PMC7079285", "section_index": 13, "section_title": "PPI Network Construction and Analysis of Selected Modules", "row_count": 6, "column_count": 5}, "table": {"label": "Table 3", "caption": "Most Significant GO Terms of the Brown Module", "rows": [["GO ID", "P-value", "No. of Genes", "Description", "Hub Gene"], ["GO:0070034", "5.09E-04", "3", "Telomerase RNA binding", "N/A"], ["GO:0035579", "5.37E-04", "5", "Specific granule membrane", "SLCO4C1"], ["GO:0002151", "7.58E-04", "2", "G-quadruplex RNA binding", "N/A"], ["GO:0006024", "7.85E-04", "5", "Glycosaminoglycan biosynthetic process", "N/A"], ["GO:0050650", "8.42E-04", "3", "Chondroitin sulfate proteoglycan biosynthetic process", "N/A"]], "row_count": 6, "column_count": 5, "numeric_cells": 15, "header_rows": 1, "locator": "section[13]/table-wrap[3]#T0003"}}], "gaps": ["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", 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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": ["GSE98793"], "resolved_accessions": ["GSE98793"], "statements": ["All of the data were freely available online, and this study did not involve any experiments on humans or animals performed by any of the authors."], "basis": "The paper names GSE98793 in NCBI 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:32214815", "data:geo:GSE98793", "asset:table:pmid:32214815:1", "asset:table:pmid:32214815:2", "asset:table:pmid:32214815:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE98793"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:52Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30623, "completion_tokens": 1467, "cached_tokens": 793}}, "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:32214815", "type": "paper", "label": "pmid:32214815"}, {"id": "source:pmid:32214815", "type": "manuscript", "label": "PMID 32214815 full text"}, {"id": "data:geo:GSE98793", "type": "dataset", "label": "GEO GSE98793"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32214815", "type": "paper", "label": "pmid:32214815"}, {"id": "source:pmid:32214815", "type": "manuscript", "label": "PMID 32214815 full text"}, {"id": "data:geo:GSE98793", "type": "dataset", "label": "GEO GSE98793"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32214815", "type": "extraction", "used": ["source:pmid:32214815"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE98793", "type": "accession_resolution", "used": ["data:geo:GSE98793"], "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:32214815", "parent_hash": "sha256:17addfbbdd23f70c8f6d9205954e3ef6acb3a3795bb50fa5c7f060c475410459", "fork_of": null, "generation": 7}, "gaps": ["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": "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": ["enesis of the disease. 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