Identification of hub genes and pathways of ferroptosis in Fusarium keratitis by bioinformatics methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36798084", "kind": "science-record", "revision": 4, "content_hash": "sha256:2498483009ee04343d45e5c85ada735bf893964b51b8c5d63ed995658273eecf", "created_at": "2026-11-01T19:01:23Z", "updated_at": "2026-11-01T22:51:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and pathways of ferroptosis in Fusarium keratitis by bioinformatics methods.", "doi": "10.3389/fcimb.2023.1103471", "pmid": "36798084", "authors": ["Xingbo Teng", "Xuewei Xiong", "Xiaoyuan Sha", "Yahui Lei", "Yuyao Diao", "Jiayan Liu", "Yuan Tian", "Lian Liu", "Jingxiang Zhong"], "journal": "Frontiers in cellular and infection microbiology", "year": 2023, "abstract": "Background: Fungal keratitis is a common blinding eye disease, and Fusarium is one of the main species that cause fungal keratitis. As is well known, oxidative stress plays an important role in Fusarium keratitis and it is also a significant initiating factor of ferroptosis. But the relationship between Fusarium keratitis and ferroptosis is currently unclear. This study aimed to speculate and validate potential ferroptosis-related genes in Fusarium keratitis using bioinformatics analysis, which provided ideas for further research on its specific mechanism and new targets for its treatment.\nMethods: The microarray expression profiling dataset (GSE58291) came from Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) were obtained by the limma package of the R software. The DEGs were performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Then, the DEGs were intersected with the genes in the ferroptosis database. The top 5 hub genes were obtained by the protein-protein interaction (PPI) network analysis and the cytoHubba plug-in of Cytoscape software. The hub genes were subjected to GSEA analysis. Then we analyzed the immune infiltration of the samples by CIBERSORT and ssGSEA algorithm. Finally, we validated the mRNA of hub genes by qPCR.\nResults: A total of 1,368 DEGs were identified and 26 ferroptosis-related DEGs were obtained. At the same time, ferroptosis-related pathways were enriched by GO and KEGG using DEGs. HMOX1, CYBB, GPX2, ALOX5 and SRC were obtained by the PPI network analysis and the cytoHubba plug-in of Cytoscape software. The iron metabolism and immune response related pathways were enriched using GSEA. They included hematopoietic cell lineage, lysosome and FC gamma R mediated phagocytosis. T cells follicular helper, monocytes, macrophages and mast cells might play an important role in Fusarium keratitis using analysis of immune infiltration. Finally, qPCR confirmed that the expression of HMOX1, CYBB, ALOX5 mRNA in the DON group was significantly elevated, while the expression of GPX2 were significantly decreased.\nConclusions: Ferroptosis may play an important role in Fusarium keratitis. HMOX1, CYBB, ALOX5 and GPX2 may be key ferroptosis-related genes in the pathogenesis of Fusarium keratitis.", "claims": [{"id": "claim-method", "statement": "The DEGs were obtained through the limma package of the R software and the cutoff criteria for statistical significance were |logFC| > 1.0 and p value < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798084", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "The DEGs were obtained through the limma package of the R software and the cutoff criteria for statistical significance were |logFC| > 1.0 and p value < 0.05."}], "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/gds/?term=gse58291 http://www.zhounan.org/ferrdb/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36798084", "locator": "sections[22] \"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/gds/?term=gse58291 http://www.zhounan.org/ferrdb/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1,368 DEGs were identified and 26 ferroptosis-related DEGs were obtained.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36798084", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 1,368 DEGs were identified and 26 ferroptosis-related DEGs were obtained."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1,368 DEGs were identified and 26 ferroptosis-related DEGs were obtained.", "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:36798084"], "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:GSE58291"], "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:GSE58291"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36798084", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcimb.2023.1103471", "sha256": "sha256:aad201f89ec15a94ee6fa546328402c3deec50160fb3d3a7bb2d42728516fabb", "bytes": 33583, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcimb.2023.1103471", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9927021", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE58291", "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=GSE58291", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58291", "version": null, "note": "Publicly available datasets were analyzed in this study. 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This data can be found here: https://www.ncbi.nlm.nih.gov/gds/?term=gse58291 http://www.zhounan.org/ferrdb/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1405992", "GSM1405993", "GSM1405994", "GSM1405995", "GSM1405996", "GSM1405997", "GSM1405998", "GSM1405999", "GSM1406000", "GSM1406001", "GSM1406002", "GSM1406003", "GSM1406004", "GSM1406005", "GSM1406006", "GSM1406007", "GSM1406008", "GSM1406009", "GSM1406010", "GSM1406011", "GSM1406012", "GSM1406013", "GSM1406014", "GSM1406015", "GSM1406016", "GSM1406017", "GSM1406018", "GSM1406019", "GSM1406020", "GSM1406021"], "sample_count": 30, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Transcriptome data for bacterial and fungal keratitis compared to cadaver cornea", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE58291 not downloaded", "asset:data:geo:GSE58291 licence not read"]}, "analysis": {"state": "partial", "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 DEGs were obtained through the limma package of the R software and the cutoff criteria for statistical significance were |logFC| > 1.0 and p value < 0.05."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-4", "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-5", "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": ["method.reader_differs_from_extractor"]}, "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. 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