Identification of 4 autophagy-related genes in heart failure by bioinformatics analysis and machine learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38347953", "kind": "science-record", "revision": 4, "content_hash": "sha256:20b6e5a5c160d34154ddd0a49a70e8b0dedb61213c74491b21a3c7efe49d27a7", "created_at": "2026-11-01T19:20:17Z", "updated_at": "2026-11-01T22:53:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of 4 autophagy-related genes in heart failure by bioinformatics analysis and machine learning.", "doi": "10.3389/fcvm.2024.1247079", "pmid": "38347953", "authors": ["Xiwei Deng", "Ziqi Yang", "Tongzheng Li", "Yang Wang", "Qinchuan Yang", "Rui An", "Jian Xu"], "journal": "Frontiers in cardiovascular medicine", "year": 2024, "abstract": "Introduction: Autophagy refers to the process of breaking down and recycling damaged or unnecessary components within a cell to maintain cellular homeostasis. Heart failure (HF) is a severe medical condition that poses a serious threat to the patient's life. Autophagy is known to play a pivotal role in the pathogenesis of HF. However, our understanding of the specific mechanisms involved remains incomplete. Here, we identify autophagy-related genes (ARGs) associated with HF, which we believe will contribute to further comprehending the pathogenesis of HF.\nMethods: By searching the GEO (Gene Expression Omnibus) database, we found the GSE57338 dataset, which was related to HF. ARGs were obtained from the HADb and HAMdb databases. Annotation of GO and enrichment analysis of KEGG pathway were carried out on the differentially expressed ARGs (AR-DEGs). We employed machine learning algorithms to conduct a thorough screening of significant genes and validated these genes by analyzing external dataset GSE76701 and conducting mouse models experimentation. At last, immune infiltration analysis was conducted, target drugs were screened and a TF regulatory network was constructed.\nResults: Through processing the dataset with R language, we obtained a total of 442 DEGs. Additionally, we retrieved 803 ARGs from the database. The intersection of these two sets resulted in 15 AR-DEGs. Upon performing functional enrichment analysis, it was discovered that these genes exhibited significant enrichment in domains related to \"regulation of cell growth\", \"icosatetraenoic acid binding\", and \"IL-17 signaling pathway\". After screening and verification, we ultimately identified 4 key genes. Finally, an analysis of immune infiltration illustrated significant discrepancies in 16 distinct types of immune cells between the HF and control group and up to 194 potential drugs and 16 TFs were identified based on the key genes.\nDiscussion: In this study, TPCN1, MAP2K1, S100A9, and CD38 were considered as key autophagy-related genes in HF. With these relevant data, further exploration of the molecular mechanisms of autophagy in HF can be carried out.", "claims": [{"id": "claim-method", "statement": "To identify differentially expressed genes (DEGs), we performed differential analysis between the HF and normal samples in GSE57338 dataset using the R package “limma” (version 3.54.2) (10).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38347953", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "To identify differentially expressed genes (DEGs), we performed differential analysis between the HF and normal samples in GSE57338 dataset using the R package “limma” (version 3.54.2) (10)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57338 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76701 Gene Expression Omnibus (GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38347953", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57338 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE76701 Gene Expression Omnibus (GEO)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified TPCN1, MAP2K1, S100A9, and CD38 as four key autophagy-related genes in heart failure.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38347953", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In this study, TPCN1, MAP2K1, S100A9, and CD38 were considered as key autophagy-related genes in HF."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified TPCN1, MAP2K1, S100A9, and CD38 as four key autophagy-related genes in heart failure.", "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:38347953"], "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:GSE57338"], "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:GSE57338"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38347953", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcvm.2024.1247079", "sha256": "sha256:4917db13269c5f3861e24a69536be6403d4b781260d833f0dcbfc4bb54f2517a", "bytes": 35692, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcvm.2024.1247079", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10859477", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57338", "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=GSE57338", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57338", "version": null, "note": "Publicly available datasets were analyzed in this study. 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