Co-Expression Network Modeling Identifies Specific Inflammation and Neurological Disease-Related Genes mRNA Modules in Mood Disorder.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35386281", "kind": "science-record", "revision": 3, "content_hash": "sha256:f0bf6591abc72d14d64fa974fb26a97ec723cd7523be4454ac9dc0fa1488d161", "created_at": "2026-11-01T18:14:12Z", "updated_at": "2026-11-01T21:27:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Co-Expression Network Modeling Identifies Specific Inflammation and Neurological Disease-Related Genes mRNA Modules in Mood Disorder.", "doi": "10.3389/fgene.2022.865015", "pmid": "35386281", "authors": ["Chunxia Yang", "Kun Zhang", "Aixia Zhang", "Ning Sun", "Zhifen Liu", "Kerang Zhang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Objectives: Mood disorders are a kind of serious mental illness, although their molecular factors involved in the pathophysiology remain unknown. One approach to examine the molecular basis of mood disorders is co-expression network analysis (WGCNA), which is expected to further divide the set of differentially expressed genes into subgroups (i.e., modules) in a more (biologically) meaningful way, fascinating the downstream enrichment analysis. The aim of our study was to identify hub genes in modules in mood disorders by using WGCNA. Methods: Microarray data for expression values of 4,311,721 mRNA in peripheral blood mononuclear cells drawn from 21 MDD, 8 BD, and 24 HC individuals were obtained from GEO (GSE39653); data for genes with expression in the bottom third for 80% or more of the samples were removed. Then, the top 70% most variable genes/probs were selected for WGCNA: 27,884 probes representing 21,840 genes; correlation between module genes and mood disorder (MDD+BD vs. HC) was evaluated. Results: About 52% of 27,765 genes were found to form 50 co-expression modules with sizes 42-3070. Among the 50 modules, the eigengenes of two modules were significantly correlated with mood disorder (p < 0.05). The saddlebrown module was found in one of the meta-modules in the network of the 50 eigengenes along with mood disorder, 6 (IER5, NFKBIZ, CITED2, TNF, SERTAD1, ADM) out of 12 differentially expressed genes identified in Savitz et al. were found in the saddlebrown module. Conclusions: We found a significant overlap for 6 hub genes (ADM, CITED2, IER5, NFKBIZ, SERTAD1, TNF) with similar co-expression and dysregulation patterns associated with mood disorder. Overall, our findings support other reports on molecular-level immune dysfunction in mood disorder and provide novel insights into the pathophysiology of mood disorder.", "claims": [{"id": "claim-method", "statement": "Using the preprocessed and transformed data, a co-expressed network was constructed using the WGCNA R package (Zhang and Horvath, 2005).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35386281", "locator": "sections[4] \"Construction of Weighted Gene Co-Expression Network\" paragraph 2", "quote": "Using the preprocessed and transformed data, a co-expressed network was constructed using the WGCNA R package (Zhang and Horvath, 2005)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: http://www.ncbi.nlm.org/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35386281", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: http://www.ncbi.nlm.org/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We found a significant overlap for 6 hub genes (ADM, CITED2, IER5, NFKBIZ, SERTAD1, TNF) with similar co-expression and dysregulation patterns associated with mood disorder.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35386281", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We found a significant overlap for 6 hub genes (ADM, CITED2, IER5, NFKBIZ, SERTAD1, TNF) with similar co-expression and dysregulation patterns associated with mood disorder."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We found a significant overlap for 6 hub genes (ADM, CITED2, IER5, NFKBIZ, SERTAD1, TNF) with similar co-expression and dysregulation patterns associated with mood disorder.", "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:35386281"], "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. 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