Identification of autophagy-related genes and immune cell infiltration characteristics in sepsis via bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37197531", "kind": "science-record", "revision": 4, "content_hash": "sha256:00a3634de6700e9a51f69ae5f9fa3889139fbfc4e3fb8744e732f34c01e85f20", "created_at": "2026-11-01T19:01:53Z", "updated_at": "2026-11-01T22:51:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of autophagy-related genes and immune cell infiltration characteristics in sepsis via bioinformatic analysis.", "doi": "10.21037/jtd-23-312", "pmid": "37197531", "authors": ["Chong Di", "Yingying Du", "Renlingzi Zhang", "Lei Zhang", "Sheng Wang"], "journal": "Journal of thoracic disease", "year": 2023, "abstract": "Background: Sepsis is a life-threatening disease with a high mortality in the intensive care unit (ICU), and autophagy plays an essential role in the development of sepsis. The purpose of this study was to identify potential autophagy-related genes in sepsis and their relationship with immune cell infiltration by bioinformatics analysis.\nMethods: The messenger RNA (mRNA) expression profile of the GSE28750 data set was collected from the Gene Expression Omnibus (GEO) database. The potential differentially expressed autophagy-related genes of sepsis were screened with the \"limma\" package in R (The Foundation for Statistical Computing). The hub genes were selected by weighted gene coexpression network analysis (WGCNA) networks with Cytoscape, and functional enrichment analysis was performed. The expression level and diagnostic value of the hub genes were validated by Wilcoxon test and receiver operating characteristic (ROC) curve analysis of the GSE95233 data set. The compositional patterns of immune cell infiltration in sepsis were estimated using the CIBERSORT algorithm. Spearman rank correlation analysis was used to associate the identified biomarkers with infiltrating immune cells. A competing endogenous (ceRNA) network was constructed to predict related noncoding RNAs of identified biomarkers with the miRWalk platform.\nResults: In all, 80 differential autophagy-related genes were obtained. GABARAPL2, GAPDH, WDFY3, MAP1LC3B, DRAM1, WIPI1, and ULK3 were identified as hub genes and diagnostic biomarker groups for sepsis. In addition, 7 differentially infiltrated immune cells correlated with the hub autophagy-related genes were identified. The ceRNA network predicted 23 microRNAs and 122 long noncoding RNAs related to 5 hub autophagy-related genes.\nConclusions: GABARAPL2, GAPDH, WDFY3, MAP1LC3B, DRAM1, WIPI1, and ULK3 may influence the development of sepsis and have a vital impact on sepsis immune regulation as autophagy-related genes.", "claims": [{"id": "claim-method", "statement": "After annotating the expression matrix, differentially expressed ARGs were screened out with the “limma” package in R software (The Foundation for Statistical Computing).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37197531", "locator": "sections[5] \"Differentially expressed analysis of the ARGs\" paragraph 2", "quote": "After annotating the expression matrix, differentially expressed ARGs were screened out with the “limma” package in R software (The Foundation for Statistical Computing)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the messenger RNA (mRNA) expression profile data sets of GSE28750 and GSE95233 from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/). The GSE28650 data set included 10 sepsis and 20 control whole blood samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37197531", "locator": "sections[4] \"ARGs and sepsis patient data sets\" paragraph 2", "quote": "We downloaded the messenger RNA (mRNA) expression profile data sets of GSE28750 and GSE95233 from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:37197531", "locator": "sections[4] \"ARGs and sepsis patient data sets\" paragraph 2", "quote": "The GSE28650 data set included 10 sepsis and 20 control whole blood samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 80 differentially expressed autophagy-related genes in sepsis, including 47 upregulated and 33 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37197531", "locator": "sections[16] \"Identification of differentially expressed ARGs (DEARGs) in sepsis\" paragraph 2", "quote": "We identified 328 ARGs from the MSigDB database and the HADb database, and 317 of these were present in the GSE28750 data set. Next, we analyzed the expression of 317 ARGs of the samples in the GSE28750 data set and identified 80 DEARGs, including 47 upregulated ARGs and 33 downregulated ARGs (Table S1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 80 differentially expressed autophagy-related genes in sepsis, including 47 upregulated and 33 downregulated genes.", "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:37197531"], "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:GSE28750"], "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:GSE28750"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37197531", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jtd-23-312", "sha256": "sha256:065ce4eb213ad67494125449afec62849920c67e471ca509ec66ad23cfcb59d1", "bytes": 36170, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jtd-23-312", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10183527", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE28750", "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=GSE28750", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28750", "version": null, "note": "We downloaded the messenger RNA (mRNA) expression profile data sets of GSE28750 and GSE95233 from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/). The GSE28650 data set included 10 sepsis and 20 control whole blood samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded the messenger RNA (mRNA) expression profile data sets of GSE28750 and GSE95233 from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/). 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The GSE28650 data set included 10 sepsis and 20 control whole blood samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded the messenger RNA (mRNA) expression profile data sets of GSE28750 and GSE95233 from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/). 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