Uncovering periodontitis-associated markers through the aggregation of transcriptomics information from diverse sources.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38919957", "kind": "science-record", "revision": 4, "content_hash": "sha256:220018df818de1f11e0fcb1a4d2f988ac6072fa46d63edf7cf162d58e1fae5a1", "created_at": "2026-11-01T20:28:59Z", "updated_at": "2026-11-01T22:54:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Uncovering periodontitis-associated markers through the aggregation of transcriptomics information from diverse sources.", "doi": "10.3389/fgene.2024.1398582", "pmid": "38919957", "authors": ["Chujun Peng", "Jinhang Huang", "Mingyue Li", "Guanru Liu", "Lingxian Liu", "Jiechun Lin", "Weijun Sun", "Hongtao Liu", "Yonghui Huang", "Xin Chen"], "journal": "Frontiers in genetics", "year": 2024, "abstract": "Introduction: Periodontitis, a common chronic inflammatory disease, significantly impacted oral health. To provide novel biological indicators for the diagnosis and treatment of periodontitis, we analyzed public microarray datasets to identify biomarkers associated with periodontitis.\nMethod: The Gene Expression Omnibus (GEO) datasets GSE16134 and GSE106090 were downloaded. We performed differential analysis and robust rank aggregation (RRA) to obtain a list of differential genes. To obtain the core modules and core genes related to periodontitis, we evaluated differential genes through enrichment analysis, correlation analysis, protein-protein interaction (PPI) network and competing endogenous RNA (ceRNA) network analysis. Potential biomarkers for periodontitis were identified through comparative analysis of dual networks (PPI network and ceRNA network). PPI network analysis was performed in STRING. The ceRNA network consisted of RRA differentially expressed messenger RNAs (RRA_DEmRNAs) and RRA differentially expressed long non-coding RNAs (RRA_DElncRNAs), which regulated each other's expression by sharing microRNA (miRNA) target sites.\nResults: RRA_DEmRNAs were significantly enriched in inflammation-related biological processes, osteoblast differentiation, inflammatory response pathways and immunomodulatory pathways. Comparing the core ceRNA module and the core PPI module, C1QA, CENPK, CENPU and BST2 were found to be the common genes of the two core modules, and C1QA was highly correlated with inflammatory functionality. C1QA and BST2 were significantly enriched in immune-regulatory pathways. Meanwhile, LINC01133 played a significant role in regulating the expression of the core genes during the pathogenesis of periodontitis.\nConclusion: The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology.", "claims": [{"id": "claim-method", "statement": "Differential analysis was performed with the help of the limma package (version 3.48.3) and differential mRNAs and differential lncRNAs of the two datasets were extracted. The ranked gene list was subsequently aggregated using the RRA () function from the RRA package (version 0.6.1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38919957", "locator": "sections[6] \"3.3 Integration and identification of differential genes\" paragraph 2", "quote": "Differential analysis was performed with the help of the limma package (version 3.48.3) and differential mRNAs and differential lncRNAs of the two datasets were extracted."}, {"asset": "source:pmid:38919957", "locator": "sections[6] \"3.3 Integration and identification of differential genes\" paragraph 2", "quote": "The ranked gene list was subsequently aggregated using the RRA () function from the RRA package (version 0.6.1)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38919957", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38919957", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The identified biomarkers C1QA, CENPK, CENPU, BST2 and LINC01133 provided valuable insight into periodontitis pathology.", "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:38919957"], "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:GSE106090"], "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:GSE106090"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38919957", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2024.1398582", "sha256": "sha256:6727bce19276965f7551f9426b9e1c7766a8347589d125e4a10439837918c24f", "bytes": 60448, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2024.1398582", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11196414", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE106090", "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=GSE106090", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE106090", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2829419", "GSM2829420", "GSM2829421", "GSM2829422", "GSM2829423", "GSM2829424", "GSM2829425", "GSM2829426", "GSM2829427", "GSM2829428", "GSM2829429", "GSM2829430", "GSM2829431", "GSM2829432", "GSM2829433", "GSM2829434", "GSM2829435", "GSM2829436"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "21827", "taxon": "Homo sapiens", "title": "Comparison of lncRNA and mRNA expression levels in peri-implantitis and periodontitis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE16134", "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=GSE16134", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16134", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:38919957", "data:geo:GSE106090"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE106090"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:22:22Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15882, "completion_tokens": 1730, "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:38919957", "type": "paper", "label": "pmid:38919957"}, {"id": "source:pmid:38919957", "type": "manuscript", "label": "PMID 38919957 full text"}, {"id": "data:geo:GSE106090", "type": "dataset", "label": "GEO GSE106090"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38919957", "type": "paper", "label": "pmid:38919957"}, {"id": "source:pmid:38919957", "type": "manuscript", "label": "PMID 38919957 full text"}, {"id": "data:geo:GSE106090", "type": "dataset", "label": "GEO GSE106090"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38919957", "type": "extraction", "used": ["source:pmid:38919957"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE106090", "type": "accession_resolution", "used": ["data:geo:GSE106090"], "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:38919957", "parent_hash": "sha256:27d0261871ff306ac8d790e553e7c4d425d8f9698714093fc75c52cd1e72c785", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE106090 licence not read", "asset:data:geo:GSE106090 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE16134 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["eatment of periodontitis, we analyzed public microarray datasets to identify biomarkers associated w"], "order_basis": "paper_text_order:288", "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": ["Differential analysis was performed with the help of the limma package (version 3.48.3) and differential mRNAs and differential lncRNAs of the two datasets were extracted. 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