Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34545294", "kind": "science-record", "revision": 8, "content_hash": "sha256:63bb9da4d78f0b945256eef4c277ce0bcb2244af3ca5c59a29016c875ced1300", "created_at": "2026-11-01T15:41:53Z", "updated_at": "2026-11-01T22:47:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Neuropeptides as Potential Crosstalks Linking Down Syndrome and Periodontitis Revealed by Transcriptomic Analyses.", "doi": "10.1155/2021/7331821", "pmid": "34545294", "authors": ["Yue Chen", "Xiaofei Yu", "Jia Kong"], "journal": "Disease markers", "year": 2021, "abstract": "BACKGROUND: This bioinformatics study was aimed to investigate the relationship between periodontitis (PD) and Down Syndrome (DS) regarding potential crosstalk genes, related neuropeptides, and biological processes.\nMETHODS: Data for PD (GSE23586, GSE10334 and GSE16134) and DS (GSE35665) were downloaded from NCBI Gene Expression Omnibus (GEO). Following normalization and merging of PD data, differential expression analysis was performed (p value < 0.05 and ∣log FC | ≥0.5). The common deregulated genes between PD and DS were considered as crosstalk genes. The significantly differentially expressed genes were used to construct the coexpression network and to further identify coexpression gene modules. To acquire the significant modules, the significant expression level of genes in the module was used to analyze the enrichment of genes in each module. Neuropeptides were assessed from NeuroPedia database. Neuropeptide genes and crosstalk genes were merged and mapped into PPI network, and the correlation coefficient (Spearman) was determined for the crosstalk genes.\nRESULTS: 138 crosstalk genes were predicted. According to the functional enrichment analysis, these genes significantly regulated different biological processes and pathways. In enrichment analysis, the significant module of DS was pink module, and turquoise module was significant in PD. Four common crosstalk genes were acquired, i.e., CD19, FCRL5, FCRLA, and HLA-DOB. In the complex network, INS and IGF2 interacted with CASP3 and TP53, which commonly regulated the MAPK signaling pathway. Moreover, the results showed that TP53 interacted with IGF2 and INS inducing the dysregulation of PI3K-Akt signaling pathway. UBL was positively correlated with crosstalk genes in both diseases. LEP was revealed to be both a neuropeptide and crosstalk gene and was positively correlated with other crosstalk genes.\nCONCLUSION: Different crosstalk genes, related neuropeptides, and biological pathways and processes were revealed between PD and DS, which can serve as a theoretical basis for future research.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed for PD and DS with the “limma” package of R project.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34545294", "locator": "sections[4] \"2.2. Differential Expression Analysis\" paragraph 2", "quote": "Differential expression analysis was performed for PD and DS with the “limma” package of R project."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34545294", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34545294"], "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": {}, "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:34545294", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/7331821", "sha256": 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"2.916247", "0.028949", "0.342906", "0.01551"], ["CLU", "Cross", "116", "2.814471", "0.036914", "0.355307", "0.012297"], ["TGFB1", "Cross", "105", "2.953883", "0.037888", "0.338537", "0.018972"], ["PDGFRB", "Cross", "100", "3.001855", "0.029277", "0.333127", "0.029775"], ["ENO2", "Cross", "98", "2.971376", "0.025504", "0.336544", "0.019222"], ["APPL1", "Cross", "94", "2.7066", "0.033818", "0.369467", "0.012009"], ["WNK1", "Cross", "92", "3.028359", "0.029407", "0.330212", "0.027433"], ["HYOU1", "Cross", "80", "2.986483", "0.020004", "0.334842", "0.023633"], ["UBC", "Cross", "72", "2.118208", "0.170684", "0.472097", "0.020807"], ["APOE", "Cross", "70", "2.999205", "0.022849", "0.333422", "0.027381"], ["ITGB2", "Cross", "62", "2.994699", "0.01851", "0.333923", "0.03201"], ["TSPAN5", "Cross", "61", "3.040021", "0.027445", "0.328945", "0.020492"], ["NOD2", "Cross", "54", "3.06626", "0.015464", "0.32613", "0.032764"], ["SERPINA1", "Cross", "52", "2.786112", "0.016528", "0.358923", 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"asset:data:geo:GSE35665 not downloaded", "asset:data:geo:GSE35665 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": "Differential expression analysis was performed for PD and DS with the “limma” package of R project."}}, {"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": "PPI"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE23586", "GSE10334", "GSE16134", "GSE35665"], "resolved_accessions": ["GSE23586", "GSE10334", "GSE16134", "GSE35665"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE23586, GSE10334, GSE16134, GSE35665 in NCBI 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:34545294", "data:geo:GSE10334", "asset:table:pmid:34545294:1", "asset:table:pmid:34545294:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10334"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:02Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28423, "completion_tokens": 1507, "cached_tokens": 9480}}, "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:34545294", "type": "paper", "label": "pmid:34545294"}, {"id": "source:pmid:34545294", "type": "manuscript", "label": "PMID 34545294 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34545294", "type": "paper", "label": "pmid:34545294"}, {"id": "source:pmid:34545294", "type": "manuscript", "label": "PMID 34545294 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34545294", "type": "extraction", "used": ["source:pmid:34545294"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10334", "type": "accession_resolution", "used": ["data:geo:GSE10334"], "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:34545294", "parent_hash": "sha256:02f9a1748b820f09f56c4dce37ac98e0d6a9667f0432c1e1278fa4f790423253", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE10334 licence not read", "asset:data:geo:GSE10334 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE16134 not downloaded", "asset:data:geo:GSE23586 licence not read", "asset:data:geo:GSE23586 not downloaded", "asset:data:geo:GSE35665 licence not read", "asset:data:geo:GSE35665 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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 expression analysis was performed for PD and DS with the “limma” package of R project."], "order_basis": "analysis_only", "id": "assay:1"}]}