Transcriptomic Analysis Reveals Genetic Cross-Talk between Periodontitis and Hypothyroidism.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35450027", "kind": "science-record", "revision": 5, "content_hash": "sha256:d039d0170308cb1e337c9f94bdd245ba70f54f1cf72fcd222729972dc60ed831", "created_at": "2026-11-01T18:14:18Z", "updated_at": "2026-11-01T22:48:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic Analysis Reveals Genetic Cross-Talk between Periodontitis and Hypothyroidism.", "doi": "10.1155/2022/5736394", "pmid": "35450027", "authors": ["Bin Yan", "Fukai Ren", "Wei Shang", "Xiaoyan Gong"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Aim of this bioinformatics study based on transcriptomic analysis was to reveal the cross-talk between periodontitis (PD) and hypothyroidism (HT).\nMethods: The gene expression datasets GSE18152 and GSE176153 of HT and GSE10334, GSE16134, and GSE173078 of PD were downloaded through the Gene Expression Omnibus (GEO) database. Differential Expression Genes (DEG) between cases and controls in each microarray were assessed by using the \"limma\" (linear models for microarray data) R package (|log2 fold change (FC)| >0 and P-value <0.05). To analyze the cross-talk effect between HT and PD, the intersection of DEG of HT and PD was selected. To investigate the biological function of cross-talk genes, the gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied. Protein-Protein Interaction (PPI) network was constructed using Cytoscape software. Top 10 cross-talk genes were screened, and the expression values of these 10 genes were extracted. ROC analysis was performed by using the pROC package and GGplot2 package of R language to predict the classification accuracy.\nResults: The overlapping DEG between HT and PD were 107 cross-talk genes. The results revealed that developmental process (P-value =1.06E-21) was the most significantly enriched biological process, followed by cell differentiation (P-value =8.49E-18) and immune system process (P-value =6.78E-11). KEGG analysis showed that Complement and coagulation cascades (P-value =2.29E-05), Hematopoietic cell lineage (P-value =2.66E-05), Phospholipase D signaling pathway (P-value =0.034367878) and Chemokine signaling pathway (P-value =0.04946333) were significantly enriched. The top 10 genes with most connections were LCE1B, LCE2B, LCE2A, LCE2C, LCE1C, LCE1F, ITGAM, C1QB, TREM2, and CD19. The AUC values of the two datasets of HT were both greater than 65% (GSE18152 = 81.42%, GSE176153 = 68.75%). AUC values of three datasets of PD were all greater than 60% (GSE10334 = 69.23%, GSE16134 = 73.72%, GSE173078 = 81.6%).\nConclusions: A genetic cross-talk between HT and PD was detected, whereby LCE family genes appeared to play the most important role.", "claims": [{"id": "claim-method", "statement": "For the microarray datasets in PD and HT, the Differential Expression Genes (DEG) were determined between cases and controls in each microarray by using the “limma” (linear models for microarray data) R package. For the high throughput sequencing datasets in PD and HT, the DEG were determined between cases and controls in each dataset by using the “DEseq2” R package. The |log2 fold change (FC)| >0 and P-value <0.05 were regarded as the cut-off criteria to determine DEG.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35450027", "locator": "sections[5] \"2.3. Differential Expression Analysis\" paragraph 2", "quote": "For the microarray datasets in PD and HT, the Differential Expression Genes (DEG) were determined between cases and controls in each microarray by using the “limma” (linear models for microarray data) R package. For the high throughput sequencing datasets in PD and HT, the DEG were determined between cases and controls in each dataset by using the “DEseq2” R package. The |log2 fold change (FC)| >0 and P-value <0.05 were regarded as the cut-off criteria to determine DEG."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35450027", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "107 differentially expressed genes overlapped between hypothyroidism and periodontitis, indicating genetic cross-talk between the two diseases.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35450027", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The overlapping DEG between HT and PD were 107 cross-talk genes."}, {"asset": "source:pmid:35450027", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "A genetic cross-talk between HT and PD was detected, whereby LCE family genes appeared to play the most important role."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "107 differentially expressed genes overlapped between hypothyroidism and periodontitis, indicating genetic cross-talk between the two diseases.", "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:35450027"], "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:GSE10334"], "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": {"fold_change": "ere defined using |log2 fold change (FC)| >0 and P-value <0"}, "inputs": ["data:geo:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35450027", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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