Identification of key genes and pathways for peri-implantitis through the analysis of gene expression data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28565775", "kind": "science-record", "revision": 9, "content_hash": "sha256:5d8ad9027572b0dab5084bbbf27cf7adf4ba0dfd984d309f8e51eec107c527af", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T22:43:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key genes and pathways for peri-implantitis through the analysis of gene expression data.", "doi": "10.3892/etm.2017.4176", "pmid": "28565775", "authors": ["Huang Zhang", "Xiong Zhang", "Jie Huang", "Xusheng Fan"], "journal": "Experimental and therapeutic medicine", "year": 2017, "abstract": "The present study attempted to identify potential key genes and pathways of peri-implantitis, and to investigate the possible mechanisms associated with it. An array data of GSE57631 was downloaded, including six samples of peri-implantitis tissue and two samples of normal tissue from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in the peri-implantitis samples compared with normal ones were analyzed with the limma package. Moreover, Gene Ontology annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEGs were performed by DAVID. A protein-protein interaction (PPI) network was established using Cytoscape software, and significant modules were analyzed using Molecular Complex Detection. A total of 819 DEGs (759 upregulated and 60 downregulated) were identified in the peri-implantitis samples compared with normal ones. Moreover, the PPI network was constructed with 413 nodes and 1,114 protein pairs. Heat shock protein HSP90AA1 (90 kDa α, member 1), a hub node with higher node degrees in module 4, was significantly enriched in antigen processing, in the presentation pathway and nucleotide-binding oligomerization domain (NOD)-like receptor-signaling pathway. In addition, nuclear factor-κ-B1 (NFKB1) was enriched in the NOD-like receptor-signaling pathway in KEGG pathway enrichment analysis for upregulated genes. The proteasome is the most significant pathway in module 1 with the highest P-value. Therefore, the results of the present study suggested that HSP90AA1 and NFKB1 may be potential key genes, and the NOD-like receptor signaling pathway and proteasome may be potential pathways associated with peri-implantitis development.", "claims": [{"id": "claim-data-access", "statement": "The array data of GSE57631 was downloaded from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database, which was deposited by Schminke et al (1). Six samples of peri-implantitis tissues and two samples of normal tissues were included in the present study. The raw data and annotation files were downloaded for subsequent analysis, based on the GPL15034 platform (Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v14]; Affymetrix, Inc., Santa Clara, CA, USA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28565775", "locator": "sections[4] \"Affymetrix microarray data\" paragraph 2", "quote": "The array data of GSE57631 was downloaded from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database, which was deposited by Schminke et al (1). Six samples of peri-implantitis tissues and two samples of normal tissues were included in the present study. The raw data and annotation files were downloaded for subsequent analysis, based on the GPL15034 platform (Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v14]; Affymetrix, Inc., Santa Clara, CA, USA)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The statistical method was the limma package with P-values calculated using a t-test, and the source-data route was downloading GSE57631 from the Gene Expression Omnibus (GEO) database. The headline result was that HSP90AA1 and NFKB1 may be key genes, while the NOD-like receptor signaling pathway and proteasome may be pathways associated with peri-implantitis development.", "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:28565775"], "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:GSE57631"], "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:GSE57631"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28565775", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/etm.2017.4176", "sha256": "sha256:f4ad2c92c360a10aa1d99b32c2a0b59ba13b2c21c3e48fd121ca54355fdaa9d3", "bytes": 18145, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/etm.2017.4176", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5443169", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE57631", "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=GSE57631", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE57631", "version": null, "note": "The array data of GSE57631 was downloaded from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database, which was deposited by Schminke et al (1). Six samples of peri-implantitis tissues and two samples of normal tissues were included in the present study. The raw data and annotation files were downloaded for subsequent analysis, based on the GPL15034 platform (Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v14]; Affymetrix, Inc., Santa Clara, CA, USA).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The array data of GSE57631 was downloaded from the Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database, which was deposited by Schminke et al (1). Six samples of peri-implantitis tissues and two samples of normal tissues were included in the present study. The raw data and annotation files were downloaded for subsequent analysis, based on the GPL15034 platform (Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v14]; Affymetrix, Inc., Santa Clara, CA, USA).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1385740", "GSM1385741", "GSM1385742", "GSM1385743", "GSM1385744", "GSM1385745", "GSM1385746", "GSM1385747"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "15034", "taxon": "Homo sapiens", "title": "Comparison of the gene expression of periimplantitis affected peri-implant tissue and healthy peri-implant tissue in vivo in human.", "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:GSE57631 not downloaded", "asset:data:geo:GSE57631 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": "The P-values of DEGs were calculated using a t-test in the limma package."}}, {"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": 0.7, "band": "medium", "quote": "pathway 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. 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