Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34727921", "kind": "science-record", "revision": 4, "content_hash": "sha256:ad54db7ed2456181110d10232415f114fe76dada26b4ec97dd1e7df293f4d3e4", "created_at": "2026-11-01T17:36:24Z", "updated_at": "2026-11-01T22:05:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma.", "doi": "10.1186/s12890-021-01711-3", "pmid": "34727921", "authors": ["Min Li", "Wenye Zhu", "Chu Wang", "Yuanyuan Zheng", "Shibo Sun", "Yan Fang", "Zhuang Luo"], "journal": "BMC pulmonary medicine", "year": 2021, "abstract": "BACKGROUND: Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of PGA is limited. In this study, we aimed to identify underlying mechanisms and hub genes of PGA.\nMETHODS: Based on the dataset from Gene Expression Omnibus(GEO), weighted gene coexpression network analysis (WGCNA), differentially expressed genes (DEGs) analysis and protein-protein interaction (PPI) network analysis were conducted to construct a gene network and to identify key gene modules and hub genes. Functional enrichment analyses were performed to investigate the biological process, pathways and immune status of PGA. The hub genes were validated in a separate dataset.\nRESULTS: Compared to non-PGA, PGA had a different gene expression pattern, in which 449 genes were differentially expressed. One gene module significantly associated with PGA was identified. Intersection between the differentially expressed genes (DEGs) and the genes from the module that were most relevant to PGA were mainly enriched in inflammation and immune response regulation. The single sample Gene Set Enrichment Analysis (ssGSEA) suggested a decreased immune infiltration and function in PGA. Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268.\nCONCLUSIONS: Our study characterized distinct gene expression patterns, biological processes and immune status of PGA and identified hub genes, which may improve the understanding of underlying mechanism and provide potential therapeutic targets for PGA.", "claims": [{"id": "claim-method", "statement": "The gene expression matrix from GSE45111 were used to perform weighted gene co-expression network analysis (WGCNA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34727921", "locator": "sections[4] \"Weighted gene co-expression network analysis\" paragraph 2", "quote": "The gene expression matrix from GSE45111 were used to perform weighted gene co-expression network analysis (WGCNA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset analyzed in this study can be derived from public repositories: GSE45111dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45111) and GSE137268 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137268).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34727921", "locator": "sections[24] \"Availability of data and materials\" paragraph 2", "quote": "The dataset analyzed in this study can be derived from public repositories: GSE45111dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45111) and GSE137268 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137268)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34727921", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268.", "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:34727921"], "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:GSE137268"], "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:GSE137268"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34727921", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12890-021-01711-3", "sha256": 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