Bioinformatics analysis combined with experiments to verify potential autophagy genes in wound healing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35845534", "kind": "science-record", "revision": 3, "content_hash": "sha256:f9b3936837b4d91af8dd8d66f2de9007f00871305b328fe0f80de0cddf2d24bf", "created_at": "2026-11-01T18:14:55Z", "updated_at": "2026-11-01T21:28:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis combined with experiments to verify potential autophagy genes in wound healing.", "doi": "10.21037/atm-22-2033", "pmid": "35845534", "authors": ["Yong-Fang Wu", "Da-Lang Fang", "Jie Wei"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: The skin is the most exposed tissue and has multiple functions. Wound healing is a major medical problem due to trauma and pathophysiological alterations suffered by patients. The aim of the present study was to search for potential autophagy genes associated with wound healing.\nMethods: The GSE168760 dataset was obtained from the Gene Expression Omnibus (GEO) database, and sequencing results were obtained for 14 patient traumas at different time periods. Differentially expressed gene (DEG) analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed. Immune cell and correlation analysis were performed for autophagy genes and DEGs. Peripheral blood was collected from patients at different time periods and Western blot (WB) assay was performed to verify autophagy genes.\nResults: A total of 226 DEGs were screened on days 0, 7, and 14, of which 162 genes were upregulated and 64 genes were downregulated. Of these, eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and retinoblastoma 1 (RB1) were autophagy-associated genes. The DEGs were mainly involved in response to virus, cellular response to type I interferon Epstein-Barr virus infection, human papillomavirus infection, ribosome, hepatitis B and RIG-I-like. EIF2AK2 and RB1 showed positive correlation with some of the immune cells, and WB showed that EIF2AK2 and RB1 proteins were significantly increased with wound healing.\nConclusions: The comprehensive analysis of GEO data in the present study provides a new theoretical basis for the molecular pathogenesis of trauma healing and potential autophagy-related therapeutic targets.", "claims": [{"id": "claim-method", "statement": "All data were expressed as mean ± standard deviation (n=3); t-tests were used to compare differences between the experimental and control groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35845534", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "All data were expressed as mean ± standard deviation (n=3); t-tests were used to compare differences between the experimental and control groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-2033/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35845534", "locator": "sections[20] \"fn-group\" paragraph 1", "quote": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-2033/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 226 DEGs were screened on days 0, 7, and 14, of which 162 genes were upregulated and 64 genes were downregulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35845534", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 226 DEGs were screened on days 0, 7, and 14, of which 162 genes were upregulated and 64 genes were downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 226 DEGs were screened on days 0, 7, and 14, of which 162 genes were upregulated and 64 genes were downregulated.", "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:35845534"], "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:GSE168760"], "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:GSE168760"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35845534", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-2033", "sha256": "sha256:7e8dbb6e07b3fd3b8d336807a980728f89fa985310629e191fdbe82a46f77eed", "bytes": 22835, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-22-2033", "version": null, "note": "Full article fetched from PMC; 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