Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29340037", "kind": "science-record", "revision": 9, "content_hash": "sha256:4751d0203a37600ee4ec1418823ab6594e050ff2f7429a39674c5568dea2b393", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T22:43:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles.", "doi": "10.18632/oncotarget.22347", "pmid": "29340037", "authors": ["Jian Wu", "Zheng-Ping Chen", "An-Quan Shang", "Wei-Wei Wang", "Zong-Ning Chen", "Yun-Juan Tao", "Yue Zhou", "Wan-Xiang Wang"], "journal": "Oncotarget", "year": 2017, "abstract": "Recurrent aphthous stomatitis (RAS) represents the most common chronic oral diseases with the prevalence ranges from 5% to 25% for different populations. Its pathogenesis remains poorly understood, which limits the development of effective drugs and treatment methods. In this study, we conducted systemic bioinformatics analysis of gene expression profiles from the Gene Expression Omnibus (GEO) to identify potential drug targets for RAS. We firstly downloaded the gene microarray datasets with the accession number of GSE37265 from GEO and performed robust multi-array (RMA) normalization with affy R programming package. Secondly, differential expression genes (DEGs) in RAS samples compared with control samples were identified based on limma package. Enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of DEGs were obtained through the Database for Annotation, Visualization and Integrated Discovery (DAVID). Finally, protein-protein interaction (PPI) network was constructed based on the combination of HPRD and BioGrid databases. What's more, we identified modules of PPI network through MCODE plugin of Cytoscape for the purpose of screening of valuable targets. As a result, 915 genes were found to be significantly differential expression in RAS samples and biological processes related to immune and inflammatory response were significantly enriched in those genes. Network and module analysis identified FBXO6, ITGA4, VCAM1 and etc as valuable therapeutic targets for RAS. Finally, FBXO6, ITGA4, and VCAM1 were further confirmed by real time RT-PCR and western blot. This study should be helpful for the research and treatment of RAS.", "claims": [{"id": "claim-method", "statement": "the normalized expression profiles were then used for the identification of differential expression genes (DEGs) in RAS samples compared with adjacent non-ulcer tissues through linear models for microarray data (limma) version3.32.2", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29340037", "locator": "sections[10] \"Differential expression analysis\" paragraph 2", "quote": "the normalized expression profiles were then used for the identification of differential expression genes (DEGs) in RAS samples compared with adjacent non-ulcer tissues through linear models for microarray data (limma) version3.32.2"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RAS gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) with deposited by Baccaglini et al with the accession number of GSE37265 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37265). A total of 33 samples, i.e. 19 adjacent non-ulcer tissue and 14 RAS samples were included in the dataset. The commercial Affymetrix Human Genome U133 Plus 2.0 Array (GEO accession no.: GPL570) was used for the quantification of genome-wide gene expression values.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29340037", "locator": "sections[9] \"Gene expression profiles\" paragraph 2", "quote": "The RAS gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) with deposited by Baccaglini et al with the accession number of GSE37265 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37265). A total of 33 samples, i.e. 19 adjacent non-ulcer tissue and 14 RAS samples were included in the dataset. The commercial Affymetrix Human Genome U133 Plus 2.0 Array (GEO accession no.: GPL570) was used for the quantification of genome-wide gene expression values."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using limma analysis of the GSE37265 microarray dataset, the study identified 915 differentially expressed genes in RAS samples, with immune- and inflammation-related biological processes enriched, and nominated FBXO6, ITGA4, and VCAM1 as potential therapeutic targets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29340037", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We firstly downloaded the gene microarray datasets with the accession number of GSE37265 from GEO and performed robust multi-array (RMA) normalization with affy R programming package. Secondly, differential expression genes (DEGs) in RAS samples compared with control samples were identified based on limma package."}, {"asset": "source:pmid:29340037", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "As a result, 915 genes were found to be significantly differential expression in RAS samples and biological processes related to immune and inflammatory response were significantly enriched in those genes."}, {"asset": "source:pmid:29340037", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Network and module analysis identified FBXO6, ITGA4, VCAM1 and etc as valuable therapeutic targets for RAS."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma analysis of the GSE37265 microarray dataset, the study identified 915 differentially expressed genes in RAS samples, with immune- and inflammation-related biological processes enriched, and nominated FBXO6, ITGA4, and VCAM1 as potential therapeutic targets.", "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:29340037"], "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:GSE37265"], "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:GSE37265"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29340037", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.22347", "sha256": "sha256:b46a988c1a6a321421a71b9745720c891e6ff1c96c4bc1f6e35ae0edad689496", "bytes": 21079, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/oncotarget.22347", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5762305", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37265", "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=GSE37265", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37265", "version": null, "note": "The RAS gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) with deposited by Baccaglini et al with the accession number of GSE37265 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37265). A total of 33 samples, i.e. 19 adjacent non-ulcer tissue and 14 RAS samples were included in the dataset. The commercial Affymetrix Human Genome U133 Plus 2.0 Array (GEO accession no.: GPL570) was used for the quantification of genome-wide gene expression values.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RAS gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) with deposited by Baccaglini et al with the accession number of GSE37265 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37265). A total of 33 samples, i.e. 19 adjacent non-ulcer tissue and 14 RAS samples were included in the dataset. The commercial Affymetrix Human Genome U133 Plus 2.0 Array (GEO accession no.: GPL570) was used for the quantification of genome-wide gene expression values.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM915126", "GSM915127", "GSM915128", "GSM915129", "GSM915130", "GSM915131", "GSM915132", "GSM915133", "GSM915134", "GSM915135", "GSM915136", "GSM915137", "GSM915138", "GSM915139", "GSM915140", "GSM915141", "GSM915142", "GSM915143", "GSM915144", "GSM915145", "GSM915146", "GSM915147", "GSM915148", "GSM915149", "GSM915150", "GSM915151", "GSM915152", "GSM915153", "GSM915154", "GSM915155", "GSM915156", "GSM915157", "GSM915158"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptome analysis of patients with recurrent aphthous stomatitis suggests novel therapeutic targets", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": 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"band": "verbatim", "quote": "the normalized expression profiles were then used for the identification of differential expression genes (DEGs) in RAS samples compared with adjacent non-ulcer tissues through linear models for microarray data (limma) version3.32.2"}}, {"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"}}], "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", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE37265"], "resolved_accessions": ["GSE37265"], "statements": ["The RAS gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) with deposited by Baccaglini et al with the accession number of GSE37265 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37265). A total of 33 samples, i.e. 19 adjacent non-ulcer tissue and 14 RAS samples were included in the dataset. The commercial Affymetrix Human Genome U133 Plus 2.0 Array (GEO accession no.: GPL570) was used for the quantification of genome-wide gene expression values."], "basis": "The paper names GSE37265 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:29340037", "data:geo:GSE37265", "asset:table:pmid:29340037:1", "asset:table:pmid:29340037:2", "asset:table:pmid:29340037:3", "asset:table:pmid:29340037:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE37265"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:24Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 49872, "completion_tokens": 2862, "cached_tokens": 18560}}, "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:29340037", "type": "paper", "label": "pmid:29340037"}, {"id": "source:pmid:29340037", "type": "manuscript", "label": "PMID 29340037 full text"}, {"id": "data:geo:GSE37265", "type": "dataset", "label": "GEO GSE37265"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29340037", "type": "paper", "label": "pmid:29340037"}, {"id": "source:pmid:29340037", "type": "manuscript", "label": "PMID 29340037 full text"}, {"id": "data:geo:GSE37265", "type": "dataset", "label": "GEO GSE37265"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29340037", "type": "extraction", "used": ["source:pmid:29340037"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE37265", "type": "accession_resolution", "used": ["data:geo:GSE37265"], "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:29340037", "parent_hash": "sha256:02294097224fbe502d1fb88c6b92bf445d5cbc52ce97fbdbaa6a580091bee3e6", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE37265 licence not read", "asset:data:geo:GSE37265 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["re further confirmed by real time RT-PCR and western blot. This study should be helpful for the resear"], "order_basis": "paper_text_order:1656", "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": ["the normalized expression profiles were then used for the identification of differential expression genes (DEGs) in RAS samples compared with adjacent non-ulcer tissues through linear models for microarray data (limma) version3.32.2"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}