Identification of ferroptosis-associated genes and potential pharmacological targets in sepsis-induced myopathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38601693", "kind": "science-record", "revision": 4, "content_hash": "sha256:fa0dcebfbe65616b27a701db94d0fb493ef2af647e0bf462074a3ef5e9bc22ce", "created_at": "2026-11-01T19:20:34Z", "updated_at": "2026-11-01T22:54:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of ferroptosis-associated genes and potential pharmacological targets in sepsis-induced myopathy.", "doi": "10.1016/j.heliyon.2024.e29062", "pmid": "38601693", "authors": ["Dongfang Wang", "Ligang Xu", "Yukun Liu", "Chuntao Wang", "Zhikai Xu", "Fan Yang", "Zhanfei Li", "Xiangjun Bai", "Yiliu Liao", "Xiangping Liu", "Yuchang Wang"], "journal": "Heliyon", "year": 2024, "abstract": "Background: The role of Ferroptosis in the course of sepsis-induced myopathy is yet unclear. The objective of our work is to identify key genes connected with Ferroptosis in sepsis-induced myopathy and investigate possible pharmaceutical targets related to this process. This research aims to provide new insights into the management of sepsis-induced myopathy.\nMethods: We got the GSE13205 dataset from the Gene Expression Omnibus (GEO) and extracted Ferroptosis-associated genes from the FerrDb database. After conducting a functional annotation analysis of these genes, we created a protein-protein interaction network using Cytoscape software to identify important genes. Subsequently, we employed CMap to investigate prospective pharmaceuticals that could target these crucial genes.\nResults: A total of 61 genes that are expressed differently (DEGs) have been found concerning Ferroptosis. These genes are involved in a wide range of biological functions, including reacting to signals from outside the cell and the availability of nutrients, programmed cell death, controlling apoptosis, and responding to peptides, chemical stressors, and hormones. The KEGG pathway study revealed that these pathways are involved in Ferroptosis, autophagy, P53 signaling, PI3K-Akt signaling, mTOR signaling, HIF-1 signaling, endocrine resistance, and different tumorigenic processes. In addition, we created a network that shows the simultaneous expression of important genes and determined the top 10 medications that have the potential to treat sepsis-induced myopathy.\nConclusion: The bioinformatics research undertaken sheds insight into the probable role of Ferroptosis-associated genes in sepsis-induced myopathy. The identified critical genes show potential as therapeutic targets for treating sepsis-induced myopathy, offering opportunities for the development of tailored medicines.", "claims": [{"id": "claim-method", "statement": "Using the “limma” package in the R software, we conducted a differential expression analysis comparing sepsis and control cohorts.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38601693", "locator": "sections[4] \"Identifying genes with differential expression related to ferroptosis\" paragraph 2", "quote": "Using the “limma” package in the R software, we conducted a differential expression analysis comparing sepsis and control cohorts."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and material used during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38601693", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The data and material used during the current study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 61 genes that are expressed differently (DEGs) have been found concerning Ferroptosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38601693", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 61 genes that are expressed differently (DEGs) have been found concerning Ferroptosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 61 genes that are expressed differently (DEGs) have been found concerning Ferroptosis.", "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:38601693"], "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:GSE13205"], "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:GSE13205"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38601693", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e29062", "sha256": "sha256:71a1a0406badf22530273a5b68bf425a4a81bc7f0936e4c25702b3967ab6e086", "bytes": 39363, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e29062", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11004882", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13205", "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=GSE13205", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13205", "version": null, "note": "The data and material used during the current study are available from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and material used during the current study are available from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM333436", "GSM333437", "GSM333438", "GSM333439", "GSM333440", "GSM333441", "GSM333442", "GSM333443", "GSM333444", "GSM333445", "GSM333446", "GSM333447", "GSM333448", "GSM333449", "GSM333450", "GSM333451", "GSM333452", "GSM333453", "GSM333454", "GSM333455", "GSM333456"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Skeletal muscle transcriptome in ICU patients suffering from sepsis induced multiple organ failure", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE13205 not downloaded", "asset:data:geo:GSE13205 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": "Using the “limma” package in the R software, we conducted a differential expression analysis comparing sepsis and control cohorts."}}, {"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": "GO 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": ["GSE13205"], "resolved_accessions": ["GSE13205"], "statements": ["The data and material used during the current study are available from the corresponding author upon reasonable request."], "basis": "The paper names GSE13205 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:38601693", "data:geo:GSE13205"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13205"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:15:13Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 11542, "completion_tokens": 1477, "cached_tokens": 256}}, "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:38601693", "type": "paper", "label": "pmid:38601693"}, {"id": "source:pmid:38601693", "type": "manuscript", "label": "PMID 38601693 full text"}, {"id": "data:geo:GSE13205", "type": "dataset", "label": "GEO GSE13205"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38601693", "type": "paper", "label": "pmid:38601693"}, {"id": "source:pmid:38601693", "type": "manuscript", "label": "PMID 38601693 full text"}, {"id": "data:geo:GSE13205", "type": "dataset", "label": "GEO GSE13205"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38601693", "type": "extraction", "used": ["source:pmid:38601693"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13205", "type": "accession_resolution", "used": ["data:geo:GSE13205"], "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:38601693", "parent_hash": "sha256:1ddaa876472fd466b7bd6aae9713f315ae9d1058bc1c41ac3645ab0879c561c5", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13205 licence not read", "asset:data:geo:GSE13205 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["utrients, programmed cell death, controlling apoptosis, and responding to peptides, chemical stress", "ternal signals, regulation of cell death and apoptosis, and responses to peptides, chemical stresso"], "order_basis": "paper_text_order:1152", "id": "assay:1"}, {"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": ["Using the “limma” package in the R software, we conducted a differential expression analysis comparing sepsis and control cohorts."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}