Identification of significant alteration genes, pathways and TFs induced by LPS in ARDS via bioinformatical analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34418997", "kind": "science-record", "revision": 7, "content_hash": "sha256:9a6df4dd947c14b6a8c2116c402b39e6dc34b3a3fddd7022745d9ee489cd6aed", "created_at": "2026-11-01T15:41:48Z", "updated_at": "2026-11-01T22:04:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of significant alteration genes, pathways and TFs induced by LPS in ARDS via bioinformatical analysis.", "doi": "10.1186/s12879-021-06578-7", "pmid": "34418997", "authors": ["Weina Lu", "Ran Ji"], "journal": "BMC infectious diseases", "year": 2021, "abstract": "BACKGROUND AND AIMS: Acute respiratory distress syndrome (ARDS) or acute lung injury (ALI) is one of the most common acute thoracopathy with complicated pathogenesis in ICU. The study is to explore the differentially expressed genes (DEGs) in the lung tissue and underlying altering mechanisms in ARDS.\nMETHODS: Gene expression profiles of GSE2411 and GSE130936 were available from GEO database, both of them included in GPL339. Then, an integrated analysis of these genes was performed, including gene ontology (GO) and KEGG pathway enrichment analysis in DAVID database, protein-protein interaction (PPI) network construction evaluated by the online database STRING, Transcription Factors (TFs) forecasting based on the Cytoscape plugin iRegulon, and their expression in varied organs in The Human Protein Atlas.\nRESULTS: A total of 39 differential expressed genes were screened from the two datasets, including 39 up-regulated genes and 0 down-regulated genes. The up-regulated genes were mainly enriched in the biological process, such as immune system process, innate immune response, inflammatory response, and also involved in some signal pathways, including cytokine-cytokine receptor interaction, Salmonella infection, Legionellosis, Chemokine, and Toll-like receptor signal pathway with an integrated analysis. GBP2, IFIT2 and IFIT3 were identified as hub genes in the lung by PPI network analysis with MCODE plug-in, as well as GO and KEGG re-enrichment. All of the three hub genes were regulated by the predictive common TFs, including STAT1, E2F1, IRF1, IRF2, and IRF9.\nCONCLUSIONS: This study implied that hub gene GBP2, IFIT2 and IFIT3, which might be regulated by STAT1, E2F1, IRF1, IRF2, or IRF9, played significant roles in ARDS. They could be potential diagnostic or therapeutic targets for ARDS patients.", "claims": [{"id": "claim-method", "statement": "DEGs between ARDS pulmonary tissues and normal pulmonary tissues were identified by online tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), with |logFC|> 2 and adjust P value < 0.05[18].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34418997", "locator": "sections[5] \"Data processing and DEGs identification\" paragraph 2", "quote": "DEGs between ARDS pulmonary tissues and normal pulmonary tissues were identified by online tool GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), with |logFC|> 2 and adjust P value < 0.05[18]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and analysed during the current study are available in the GEO datasets repository, (https://www.ncbi.nlm.nih.gov/geo/).The datasets generated and analysed during the current study are available in the STRING repository, (https://string-db.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34418997", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets generated and analysed during the current study are available in the GEO datasets repository, (https://www.ncbi.nlm.nih.gov/geo/).The datasets generated and analysed during the current study are available in the STRING repository, (https://string-db.org/)."}], "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:34418997"], "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:GSE130936"], "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:GSE130936"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34418997", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12879-021-06578-7", "sha256": 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