Gene expression profile analysis of severe influenza-based modulation of idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39420432", "kind": "science-record", "revision": 4, "content_hash": "sha256:86d254417e5bae1b9576c18a0fb117d0d07f09d0509a9aeb2fd89c2108a150bf", "created_at": "2026-11-01T20:29:39Z", "updated_at": "2026-11-01T22:55:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profile analysis of severe influenza-based modulation of idiopathic pulmonary fibrosis.", "doi": "10.1186/s40001-024-02107-9", "pmid": "39420432", "authors": ["Jianping Kong", "Liang Chen"], "journal": "European journal of medical research", "year": 2024, "abstract": "BACKGROUND: It is known severe influenza infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other. Till now, no associated mechanism has been reported.\nMETHOD: We collected the genetic pattern of expression of severe influenza (GSE111368) and IPF (GSE70866) from the Gene Expression Omnibus (GEO) database. Common differentially expressed genes (C-DEGs) were identified from the two datasets, and using this data, we conducted three forms of analyses, functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis.\nRESULTS: In all, 174 C-DEGs were selected for additional analyses. Based on our functional analysis, these C-DEGs mediated inflammatory response and cell differentiation. Furthermore, using cytoHubba, we identified 15 genes, namely, MELK, HJURP, BIRC5, TPX2, TK1, CDT1, UBE2C, UHRF1, CCNA2, TYMS, CDCA5, CDCA8, RAD54L, CCNB2, and ITGAM, which served as hub genes to possibly contribute to severe influenza patients with IPF disease as comorbidity. The hub gene expressions were further confirmed using two stand-alone datasets (GSE101702 for severe influenza and GSE10667 for IPF).\nCONCLUSION: Herein, we demonstrated the significance of common pathways and critical genes in severe influenza and IPF etiologies. The identified pathways and genes may be employed as possible therapeutic targets for future therapy against severe influenza patients with IPF.", "claims": [{"id": "claim-method", "statement": "Training dataset normalization and probe annotation was conducted using the R (v. 4.2.3) ‘GEOquery’ and ‘limma’ packages (v. 3.52.4). DEGs identification employed criteria as follows: adjusted P < 0.05 and logFC > 0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39420432", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "Training dataset normalization and probe annotation was conducted using the R (v. 4.2.3) ‘GEOquery’ and ‘limma’ packages (v. 3.52.4). DEGs identification employed criteria as follows: adjusted P < 0.05 and logFC > 0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39420432", "locator": "sections[27] \"notes\" paragraph 1", "quote": "Publicly available datasets were analyzed in this study. These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 174 common differentially expressed genes between severe influenza and IPF.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39420432", "locator": "sections[12] \"Identification of DEGs\" paragraph 2", "quote": "Subsequently, employing the Venn diagram, we identified 174 C-DEGs, which included 94 highly and 80 scarcely expressed genes (Fig. 2c and Supplementary file 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 174 common differentially expressed genes between severe influenza and IPF.", "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:39420432"], "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:GSE101702"], "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:GSE101702"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39420432", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-024-02107-9", "sha256": "sha256:afa3a451d6d170604cdb97bf98fe3f2b228412f6a4c6a6445041411cf0aadc4c", "bytes": 27447, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-024-02107-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11488079", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101702", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101702", "version": null, "note": "Publicly available datasets were analyzed in this study. These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2712389", "GSM2712390", "GSM2712391", "GSM2712392", "GSM2712393", "GSM2712394", "GSM2712395", "GSM2712396", "GSM2712397", "GSM2712398", "GSM2712399", "GSM2712400", "GSM2712401", "GSM2712402", "GSM2712403", "GSM2712404", "GSM2712405", "GSM2712406", "GSM2712407", "GSM2712408", "GSM2712409", "GSM2712410", "GSM2712411", "GSM2712412", "GSM2712413", "GSM2712414", "GSM2712415", "GSM2712416", "GSM2712417", "GSM2712418", "GSM2712419", "GSM2712420", "GSM2712421", "GSM2712422", "GSM2712423", "GSM2712424", "GSM2712425", "GSM2712426", "GSM2712427", "GSM2712428", "GSM2712429", "GSM2712430", "GSM2712431", "GSM2712432", "GSM2712433", "GSM2712434", "GSM2712435", "GSM2712436", "GSM2712437", "GSM2712438", "GSM2712439", "GSM2712440", "GSM2712441", "GSM2712442", "GSM2712443", "GSM2712444", "GSM2712445", "GSM2712446", "GSM2712447", "GSM2712448", "GSM2712449", "GSM2712450", "GSM2712451", "GSM2712452", "GSM2712453", "GSM2712454", "GSM2712455", "GSM2712456", "GSM2712457", "GSM2712458", "GSM2712459", "GSM2712460", "GSM2712461", "GSM2712462", "GSM2712463", "GSM2712464", "GSM2712465", "GSM2712466", "GSM2712467", "GSM2712468", "GSM2712469", "GSM2712470", "GSM2712471", "GSM2712472", "GSM2712473", "GSM2712474", "GSM2712475", "GSM2712476", "GSM2712477", "GSM2712478", "GSM2712479", "GSM2712480", "GSM2712481", "GSM2712482", "GSM2712483", "GSM2712484", "GSM2712485", "GSM2712486", "GSM2712487", "GSM2712488", "GSM2712489", "GSM2712490", "GSM2712491", "GSM2712492", "GSM2712493", "GSM2712494", "GSM2712495", "GSM2712496", "GSM2712497", "GSM2712498", "GSM2712499", "GSM2712500", "GSM2712501", "GSM2712502", "GSM2712503", "GSM2712504", "GSM2712505", "GSM2712506", "GSM2712507", "GSM2712508", "GSM2712509", "GSM2712510", "GSM2712511", "GSM2712512", "GSM2712513", "GSM2712514", "GSM2712515", "GSM2712516", "GSM2712517", "GSM2712518", "GSM2712519", "GSM2712520", "GSM2712521", "GSM2712522", "GSM2712523", "GSM2712524", "GSM2712525", "GSM2712526", "GSM2712527", "GSM2712528", "GSM2712529", "GSM2712530", "GSM2712531", "GSM2712532", "GSM2712533", "GSM2712534", "GSM2712535", "GSM2712536", "GSM2712537", "GSM2712538", "GSM2712539", "GSM2712540", "GSM2712541", "GSM2712542", "GSM2712543", "GSM2712544", "GSM2712545", "GSM2712546", "GSM2712547"], "sample_count": 159, "group_sizes": null, "group_sizes_basis": null, "platform": "21185", "taxon": "Homo sapiens", "title": "Host response to IAV infections in human patients", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE10667", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10667", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10667", "version": null, "note": "Publicly available datasets were analyzed in this study. These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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These data can be found in GSE111368 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111368), GSE101702 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101702), GSE70866 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70866) and GSE10667 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1820719", "GSM1820720", "GSM1820721", "GSM1820722", "GSM1820723", "GSM1820724", "GSM1820725", "GSM1820726", "GSM1820727", "GSM1820728", "GSM1820729", "GSM1820730", "GSM1820731", "GSM1820732", "GSM1820733", "GSM1820734", "GSM1820735", "GSM1820736", "GSM1820737", "GSM1820738", "GSM1820739", "GSM1820740", "GSM1820741", "GSM1820742", "GSM1820743", "GSM1820744", "GSM1820745", "GSM1820746", "GSM1820747", "GSM1820748", "GSM1820749", "GSM1820750", "GSM1820751", "GSM1820752", "GSM1820753", "GSM1820754", "GSM1820755", "GSM1820756", "GSM1820757", "GSM1820758", "GSM1820759", "GSM1820760", "GSM1820761", "GSM1820762", "GSM1820763", "GSM1820764", "GSM1820765", "GSM1820766", "GSM1820767", "GSM1820768", "GSM1820769", "GSM1820770", "GSM1820771", "GSM1820772", "GSM1820773", "GSM1820774", "GSM1820775", "GSM1820776", "GSM1820777", "GSM1820778", "GSM1820779", "GSM1820780", "GSM1820781", "GSM1820782", "GSM1820783", "GSM1820784", "GSM1820785", "GSM1820786", "GSM1820787", "GSM1820788", "GSM1820789", "GSM1820790", "GSM1820791", "GSM1820792", "GSM1820793", "GSM1820794", "GSM1820795", "GSM1820796", "GSM1820797", "GSM1820798", "GSM1820799", "GSM1820800", "GSM1820801", "GSM1820802", "GSM1820803", "GSM1820804", "GSM1820805", "GSM1820806", "GSM1820807", "GSM1820808", "GSM1820809", "GSM1820810", "GSM1820811", "GSM1820812", "GSM1820813", "GSM1820814", "GSM1820815", "GSM1820816", "GSM1820817", "GSM1820818", "GSM1820819", "GSM1820820", "GSM1820821", "GSM1820822", "GSM1820823", "GSM1820824", "GSM1820825", "GSM1820826", "GSM1820827", "GSM1820828", "GSM1820829", "GSM1820830", "GSM1820831", "GSM1820832", "GSM1820833", "GSM1820834", "GSM1820835", "GSM1820836", "GSM1820837", "GSM1820838", "GSM1820839", "GSM1820840", "GSM1820841", "GSM1820842", "GSM1820843", "GSM1820844", "GSM1820845", "GSM1820846", "GSM1820847", "GSM1820848", "GSM1820849", "GSM1820850", "GSM1820851", "GSM1820852", "GSM1820853", "GSM1820854", "GSM1820855", "GSM1820856", "GSM1820857", "GSM1820858", "GSM1820859", "GSM1820860", "GSM1820861", "GSM1820862", "GSM1820863", "GSM1820864", "GSM1820865", "GSM1820866", "GSM1820867", "GSM1820868", "GSM1820869", "GSM1820870", "GSM1820871", "GSM1820872", "GSM1820873", "GSM1820874", "GSM1820875", "GSM1820876", "GSM1820877", "GSM1820878", "GSM1820879", "GSM1820880", "GSM1820881", "GSM1820882", "GSM1820883", "GSM1820884", "GSM1820885", "GSM1820886", "GSM1820887", "GSM1820888", "GSM1820889", "GSM1820890", "GSM1820891", "GSM1820892", "GSM1820893", "GSM1820894", "GSM1820895", "GSM1820896", "GSM1820897", "GSM1820898", "GSM1820899", "GSM1820900", "GSM1820901", "GSM1820902", "GSM1820903", "GSM1820904", "GSM1820905", "GSM1820906", "GSM1820907", "GSM1820908", "GSM1820909", "GSM1820910", "GSM1820911", "GSM1820912", "GSM1820913", "GSM1820914"], "sample_count": 196, "group_sizes": null, "group_sizes_basis": null, "platform": "17077;14550", "taxon": "Homo sapiens", "title": "BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (II)", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE101702 not downloaded", "asset:data:geo:GSE101702 licence not read", "asset:data:geo:GSE10667 not downloaded", "asset:data:geo:GSE10667 licence not read", "asset:data:geo:GSE111368 not downloaded", "asset:data:geo:GSE111368 licence not read", "asset:data:geo:GSE70866 not downloaded", "asset:data:geo:GSE70866 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Training dataset normalization and probe annotation was conducted using the R (v. 4.2.3) ‘GEOquery’ and ‘limma’ packages (v. 3.52.4). 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DEGs identification employed criteria as follows: adjusted P < 0.05 and logFC > 0.5."], "order_basis": "analysis_only", "id": "assay:1"}]}