Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34946949", "kind": "science-record", "revision": 3, "content_hash": "sha256:f77c0d35e9044882eaa076a7ee4e35a0b07c9693d908fa3752e77736549b3579", "created_at": "2026-11-01T17:36:39Z", "updated_at": "2026-11-01T21:26:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome.", "doi": "10.3390/genes12122000", "pmid": "34946949", "authors": ["Alejandra Rodríguez-Ortiz", "Julio César Montoya-Villegas", "Felipe García-Vallejo", "Yecid Mina-Paz"], "journal": "Genes", "year": 2021, "abstract": "DNA methylation and histone posttranslational modifications are epigenetics processes that contribute to neurophenotype of Down Syndrome (DS). Previous reports present strong evidence that nonhistone high-mobility-group N proteins (HMGN) are epigenetic regulators. They play important functions in various process to maintain homeostasis in the brain. We aimed to analyze the differential expression of five human HMGN genes in some brain structures and age ranks from DS postmortem brain samples. Methodology: We performed a computational analysis of the expression of human HMGN from the data of a DNA microarray experiment (GEO database ID GSE59630). Using the transformed log2 data, we analyzed the differential expression of five HMGN genes in several brain areas associated with cognition in patients with DS. Moreover, using information from different genome databases, we explored the co-expression and protein interactions of HMNGs with the histones of nucleosome core particle and linker H1 histone. Results: We registered that HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients. Age-rank comparisons between euploid control and DS individuals showed that HMGN2 and HMGN4 were overexpressed in the DS brain at 16 to 22 gestation weeks. From the BioGRID database, we registered high interaction scores of HMGN2 and HMGN4 with Hist1H1A and Hist1H3A. Conclusions: Overall, our results give strong evidence to propose that DS would be an epigenetics-based aneuploidy. Remodeling brain chromatin by HMGN1 and HMGN5 would be an essential pathway in the modification of brain homeostasis in DS.", "claims": [{"id": "claim-method", "statement": "The Z test/Two-tailed was used to calculate differences in HMGN differential expression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34946949", "locator": "sections[9] \"2.7. Statistical Analysis\" paragraph 2", "quote": "The Z test/Two-tailed was used to calculate differences in HMGN differential expression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "DNA microarray experiment whose registration code in the GEO database is GSE59630 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59630 (accessed on 1 December 2018)).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34946949", "locator": "sections[23] \"notes\" paragraph 1", "quote": "DNA microarray experiment whose registration code in the GEO database is GSE59630 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59630 (accessed on 1 December 2018))."}], "state": "complete"}, {"id": "claim-target-result", "statement": "HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34946949", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We registered that HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients.", "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:34946949"], "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:GSE59630"], "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:GSE59630"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34946949", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes12122000", "sha256": "sha256:7a85813fbc74c0007fc4310a2947c0a5faa5fe39833ae80103af6694a7d119d5", "bytes": 22276, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes12122000", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8700945", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59630", "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=GSE59630", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59630", "version": null, "note": "DNA microarray experiment whose registration code in the GEO database is GSE59630 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59630 (accessed on 1 December 2018)).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "DNA microarray experiment whose registration code in the GEO database is GSE59630 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59630 (accessed on 1 December 2018)).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1440797", "GSM1440798", "GSM1440799", "GSM1440800", "GSM1440801", "GSM1440802", "GSM1440803", "GSM1440804", "GSM1440805", "GSM1440806", "GSM1440807", "GSM1440808", "GSM1440809", "GSM1440810", "GSM1440811", "GSM1440812", "GSM1440813", "GSM1440814", "GSM1440815", "GSM1440816", "GSM1440817", "GSM1440818", "GSM1440819", "GSM1440820", "GSM1440821", "GSM1440822", "GSM1440823", "GSM1440824", "GSM1440825", "GSM1440826", "GSM1440827", "GSM1440828", "GSM1440829", "GSM1440830", "GSM1440831", "GSM1440832", "GSM1440833", "GSM1440834", "GSM1440835", "GSM1440836", "GSM1440837", "GSM1440838", "GSM1440839", "GSM1440840", "GSM1440841", "GSM1440842", "GSM1440843", "GSM1440844", "GSM1440845", "GSM1440846", "GSM1440847", "GSM1440848", "GSM1440849", "GSM1440850", "GSM1440851", "GSM1440852", "GSM1440853", "GSM1440854", "GSM1440855", "GSM1440856", "GSM1440857", "GSM1440858", "GSM1440859", "GSM1440860", "GSM1440861", "GSM1440862", "GSM1440863", "GSM1440864", "GSM1440865", "GSM1440866", "GSM1440867", "GSM1440868", "GSM1440869", "GSM1440870", "GSM1440871", "GSM1440872", "GSM1440873", "GSM1440874", "GSM1440875", "GSM1440876", "GSM1440877", "GSM1440878", "GSM1440879", "GSM1440880", "GSM1440881", "GSM1440882", "GSM1440883", "GSM1440884", "GSM1440885", "GSM1440886", "GSM1440887", "GSM1440888", "GSM1440889", "GSM1440890", "GSM1440891", "GSM1440892", "GSM1440893", "GSM1440894", "GSM1440895", "GSM1440896", "GSM1440897", "GSM1440898", "GSM1440899", "GSM1440900", "GSM1440901", "GSM1440902", "GSM1440903", "GSM1440904", "GSM1440905", "GSM1440906", "GSM1440907", "GSM1440908", "GSM1440909", "GSM1440910", "GSM1440911", "GSM1440912"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Longitudinal Gene Expression Analysis in Human Brain identifies biological processes underlying neuropathology in Down Syndrome", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE59630 not downloaded", "asset:data:geo:GSE59630 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Z test/Two-tailed", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Z test/Two-tailed was used to calculate differences in HMGN differential expression."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Z test/Two-tailed), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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