Bioinformatics analysis of the potential biomarkers for acute respiratory distress syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32856055", "kind": "science-record", "revision": 9, "content_hash": "sha256:745241b5f019678b0eba0d5403e158fdde75bfd0d4393d986af94102e8de54a9", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of the potential biomarkers for acute respiratory distress syndrome.", "doi": "10.1042/BSR20192436", "pmid": "32856055", "authors": ["Lin Liao", "Pinhu Liao"], "journal": "Bioscience reports", "year": 2020, "abstract": "BACKGROUND: Acute respiratory distress syndrome (ARDS) is caused by uncontrolled inflammation, and the activation of alveolar macrophages (AM) is involved in pathophysiologic procedures. The present study aimed to identify key AM genes and pathways and try to provide potential targets for prognosis and early intervention in ARDS.\nMETHODS: The mRNA expression profile of GSE89953 was obtained from the Gene Expression Omnibus database. The LIMMA package in R software was used to identify differentially expressed genes (DEGs), and the clusterProfiler package was used for functional enrichment and pathway analyses. A protein-protein interaction network of DEGs was constructed to identify hub genes via the STRING database and Cytoscape software. Hub gene expression was validated using differentially expressed proteins (DEPs) obtained from the ProteomeXchange datasets to screen potential biomarkers.\nRESULTS: A total of 166 DEGs (101 up-regulated and 65 down-regulated) were identified. The up-regulated DEGs were mainly enriched in regulation of the ERK1 and ERK2 cascade, response to interferon-gamma, cell chemotaxis, and migration in biological processes. In the KEGG pathway analysis, up-regulated DEGs were mainly involved in rheumatoid arthritis, cytokine-cytokine receptor interactions, phagosome, and the chemokine signaling pathway. The 12 hub genes identified included GZMA, MPO, PRF1, CXCL8, ELANE, GZMB, SELL, APOE, SPP1, JUN, CD247, and CCL2.\nCONCLUSION: SPP1 was consistently differentially expressed in both DEGs and DEPs. SPP1 could be a potential biomarker for ARDS.", "claims": [{"id": "claim-method", "statement": "The LIMMA package (version 3.38.3) in R software was used to identify DEGs between paired AM and MONO samples in 26 ARDS patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32856055", "locator": "sections[4] \"Differentially expressed genes identifying\" paragraph 2", "quote": "The LIMMA package (version 3.38.3) in R software was used to identify DEGs between paired AM and MONO samples in 26 ARDS patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32856055", "locator": "sections[3] \"Overview of data\" paragraph 2", "quote": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database."}], "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:32856055"], "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:GSE89953"], "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:GSE89953"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32856055", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20192436", "sha256": "sha256:734b4e8e7febb97baee0a5b68f879d33ae34981f9ae7edaccd9739f65d1e8826", "bytes": 14773, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1042/BSR20192436", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7475302", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE89953", "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=GSE89953", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE89953", "version": null, "note": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2544450", "GSM2544451", "GSM2544452", "GSM2544453", "GSM2544454", "GSM2544455", "GSM2544456", "GSM2544457", "GSM2544458", "GSM2544459", "GSM2544460", "GSM2544461", "GSM2544462", "GSM2544463", "GSM2544464", "GSM2544465", "GSM2544466", "GSM2544467", "GSM2544468", "GSM2544469", "GSM2544470", "GSM2544471", "GSM2544472", "GSM2544473", "GSM2544474", "GSM2544475", "GSM2544476", "GSM2544477", "GSM2544478", "GSM2544479", "GSM2544480", "GSM2544481", "GSM2544482", "GSM2544483", "GSM2544484", "GSM2544485", "GSM2544486", "GSM2544487", "GSM2544488", "GSM2544489", "GSM2544490", "GSM2544491", "GSM2544492", "GSM2544493", "GSM2544494", "GSM2544495", "GSM2544496", "GSM2544497", "GSM2544498", "GSM2544499", "GSM2544500", "GSM2544501"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "6883", "taxon": "Homo sapiens", "title": "Transcriptomics of Human Alveolar Macrophages and Peripheral Blood Monocytes in Acute Respiratory Distress Syndrome", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PXD002672", "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=PXD002672", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD002672", "version": null, "note": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Prediction of Mortality In Acute Respiratory Distress Syndrome", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32856055:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f4dbd56cea9e808e294f6468a12c4accb96d4e9cd69d193e0dc9f8989bc963aa", "bytes": 1059, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Pathway enrichment analysis of DEGs", "structure": {"pmcid": "PMC7475302", "section_index": 10, "section_title": "Gene Ontology analysis and pathway enrichment analysis of DEGs", "row_count": 13, "column_count": 5}, "table": {"label": "Table 1", "caption": "Pathway enrichment analysis of DEGs", "rows": [["Expression", "Pathway ID", "Description", "P-value", "Count"], ["Up-regulated", "hsa05323", "Rheumatoid arthritis", "1.04 × 10−09", "10"], ["", "hsa05133", "Pertussis", "1.37 × 10−06", "7"], ["", "hsa04145", "Phagosome", "1.66 × 10−06", "9"], ["", "hsa05150", "Staphylococcus aureus infection", "1.06 × 10−05", "6"], ["", "hsa05142", "Chagas disease (American trypanosomiasis)", "1.06 × 10−05", "7"], ["", "hsa03320", "PPAR signaling pathway", "1.73 × 10−05", "6"], ["", "hsa05140", "Leishmaniasis", "1.73 × 10−05", "6"], ["", "hsa04610", "Complement and coagulation cascades", "2.52 × 10−05", "6"], ["", "hsa04060", "Cytokine–cytokine receptor interaction", "5.73 × 10−05", "10"], ["", "hsa04062", "Chemokine signaling pathway", "7.82 × 10−05", "8"], ["Down-regulated", "hsa04650", "Natural killer cell mediated cytotoxicity", "4.87 × 10−05", "5"], ["", "hsa05144", "Malaria", "4.77 × 10−04", "3"]], "row_count": 13, "column_count": 5, "numeric_cells": 36, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE89953 not downloaded", "asset:data:geo:GSE89953 licence not read", "asset:data:geo:PXD002672 not downloaded", "asset:data:geo:PXD002672 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": "The LIMMA package (version 3.38.3) in R software was used to identify DEGs between paired AM and MONO samples in 26 ARDS patients."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE89953", "PXD002672"], "resolved_accessions": ["GSE89953", "PXD002672"], "statements": ["The mRNA expression profile of GSE89953 was downloaded from the GEO (http://www.ncbi.nlm.nih.gov/geo) database."], "basis": "The paper names GSE89953, PXD002672 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32856055", "data:geo:GSE89953", "asset:table:pmid:32856055:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE89953"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:11Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 11690, "completion_tokens": 1259, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32856055", "type": "paper", "label": "pmid:32856055"}, {"id": "source:pmid:32856055", "type": "manuscript", "label": "PMID 32856055 full text"}, {"id": "data:geo:GSE89953", "type": "dataset", "label": "GEO GSE89953"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32856055", "type": "paper", "label": "pmid:32856055"}, {"id": "source:pmid:32856055", "type": "manuscript", "label": "PMID 32856055 full text"}, {"id": "data:geo:GSE89953", "type": "dataset", "label": "GEO GSE89953"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32856055", "type": "extraction", "used": ["source:pmid:32856055"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE89953", "type": "accession_resolution", "used": ["data:geo:GSE89953"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32856055", "parent_hash": "sha256:47f502e1b9da0ba69edc179ec1438ddbda41aecf29128f63123f55799a392060", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE89953 licence not read", "asset:data:geo:GSE89953 not downloaded", "asset:data:geo:PXD002672 licence not read", "asset:data:geo:PXD002672 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The LIMMA package (version 3.38.3) in R software was used to identify DEGs between paired AM and MONO samples in 26 ARDS patients."], "order_basis": "analysis_only", "id": "assay:1"}]}