Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31419013", "kind": "science-record", "revision": 6, "content_hash": "sha256:ac149952a58454f53fb58b081013c0cf51e2403f93cb4bd01120f3e8e4510f97", "created_at": "2026-11-01T15:40:48Z", "updated_at": "2026-11-01T21:22:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease.", "doi": "10.1111/jcmm.14585", "pmid": "31419013", "authors": ["Jiangyue Qin", "Ting Yang", "Ni Zeng", "Chun Wan", "Lijuan Gao", "Xiaoou Li", "Lei Chen", "Yongchun Shen", "Fuqiang Wen"], "journal": "Journal of cellular and molecular medicine", "year": 2019, "abstract": "Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with multiple molecular mechanisms. To investigate and contrast the molecular processes differing between bronchiolitis and emphysema phenotypes of COPD, we downloaded the GSE69818 microarray data set from the Gene Expression Omnibus (GEO), which based on lung tissues from 38 patients with emphysema and 32 patients with bronchiolitis. Then, weighted gene coexpression network analysis (WGCNA) and differential coexpression (DiffCoEx) analysis were performed, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment analysis (KEGG) analysis. Modules and hub genes for bronchiolitis and emphysema were identified, and we found that genes in modules linked to neutrophil degranulation, Rho protein signal transduction and B cell receptor signalling were coexpressed in emphysema. DiffCoEx analysis showed that four hub genes (IFT88, CCDC103, MMP10 and Bik) were consistently expressed in emphysema patients; these hub genes were enriched, respectively, for functions of cilium assembly and movement, proteolysis and apoptotic mitochondrial changes. In our re-analysis of GSE69818, gene expression networks in relation to emphysema deepen insights into the molecular mechanism of COPD and also identify some promising therapeutic targets.", "claims": [{"id": "claim-data-access", "statement": "All data used to support the findings of the current study are available from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69818).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31419013", "locator": "sections[23] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "All data used to support the findings of the current study are available from Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69818)."}], "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:31419013"], "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:GSE69818"], "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:GSE69818"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31419013", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.14585", "sha256": 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"CCDC103, IFT88, BIK, DCDC2B, BEST4, TCTEX1D4, CLCA2, GBP6, VTCN1, SPATA17, TEKT4, TTC30A, CERKL, CFAP65, FBXL2, ALDH1L1, NME9, ANKUB1, WDR49, CEP19, UGT2A1, ADH6, HSPA4L, SLC23A1, GABRP, ARMC2, LRWD1, IQUB, NUP62CL, CCDC160, FZD3, PSCA, TCN1, LRRC10B, LRTOMT, DNAJB13, MMP10, PIH1D2, MEIG1, COL17A1, PLEKHG7, CCDC60, MORN3, ABHD12B, CKMT1B, GCNT3, ZG16B, C16orf46, B9D1, FAM187A, KIF19, KATNAL2, SPEF1, TNFAIP8L1, CYP2F1, KCNE1, TMPRSS3"], ["Blue", "KIF2C, DEPDC1, KIF14, SPC25, CSPG5, CCNA2, CCNB1, KIF4B, TCF19, ANLN, KIF4A, CCNE2, PHF19, KIF23, PRC1, SHCBP1, ORC6, AURKB, BIRC5, SKA1, CCNE1, CDC45"], ["Brown", "PLA2G2D, TRIM63, FCMR, DAPL1, CHRNA1, KLHL6, TM4SF19, HRK, OTOA, SLC16A6"], ["Green", "SLC25A33, RLF, BZW1P2, CSNK1A1, RNF19A, AAED1, NAB2, CRY1, ZNF410, PLAUR"], ["Yellow", "GNL2, VCAM1, BATF3, HRH1, DNAJC25, SDHAF2, HAPLN3, TOP1, PPAN‐P2RY11, BCL3"]], "row_count": 6, "column_count": 2, "numeric_cells": 5, "header_rows": 1, "locator": 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