Integrated Quantitative Neuro-Transcriptome Analysis of Several Brain Areas in Human Trisomy 21.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35456434", "kind": "science-record", "revision": 4, "content_hash": "sha256:e1c62f22a1a656a44e2c925518a74adce193817989602de477f774e78b2d67bd", "created_at": "2026-11-01T18:14:18Z", "updated_at": "2026-11-01T22:06:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Quantitative Neuro-Transcriptome Analysis of Several Brain Areas in Human Trisomy 21.", "doi": "10.3390/genes13040628", "pmid": "35456434", "authors": ["Alejandra Rodríguez-Ortiz", "Julio César Montoya-Villegas", "Felipe García-Vallejo", "Yecid Mina-Paz"], "journal": "Genes", "year": 2022, "abstract": "BACKGROUND: Although Down syndrome (DS) is the most frequent human chromosomal disorder and it causes mainly intellectual disability, its clinical presentation is complex and variable.\nOBJECTIVE: We aimed to analyze and compare the transcriptome disruption in several brain areas from individuals with DS and euploid controls as a new approach to consider a global systemic differential disruption of gene expression beyond chromosome 21.\nMETHODS: We used data from a DNA microarray experiment with ID GSE59630 previously deposited in the GEO DataSet of NCBI database. The array contained log2 values of 17,537 human genes expressed in several aeras of the human brain. We calculated the differential gene expression (Z-ratio) of all genes.\nRESULTS: We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes. Moreover, we registered the lowest Z-ratio correlation between the age ranks of 16-22 weeks of gestation and 39-42 years (R2 = 0.06) and the highest Z-ratio correlation between the age ranks of 30-39 years and 40-42 years (R2 = 0.89). The analysis per brain areas showed that the hippocampus and the cerebellar cortex had the most different gene expression pattern when compared to the brain as a whole.\nCONCLUSIONS: Our results support the hypothesis of a systemic imbalance of brain protein homeostasis, or proteostasis network of cognitive and neuroplasticity process, as new model to explain the important effect on the neurophenotype of trisomy that occur not only in the loci of chromosome 21 but also in genes located in other chromosomes.", "claims": [{"id": "claim-method", "statement": "The Wilcoxon signed-rank test/Two-tailed was used to calculate differences between medians of two samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35456434", "locator": "sections[5] \"2.3. Statistical Analysis\" paragraph 2", "quote": "The Wilcoxon signed-rank test/Two-tailed was used to calculate differences between medians of two samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article. 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:35456434", "locator": "sections[17] \"notes\" paragraph 1", "quote": "All data generated or analysed during this study are included in this published article. 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": "We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35456434", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We found several differences in gene expression along the DS brain transcriptome, not only in the genes located at chromosome 21 but in other chromosomes.", "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:35456434"], "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": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35456434", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/genes13040628", "sha256": "sha256:2e6c290f118153e532d3c87f94f930d025feec4593de88ac077be71791a3922c", "bytes": 20640, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/genes13040628", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9033037", "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": "All data generated or analysed during this study are included in this published article. 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": "All data generated or analysed during this study are included in this published article. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE59630"], "resolved_accessions": ["GSE59630"], "statements": ["All data generated or analysed during this study are included in this published article. 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))."], "basis": "The paper names GSE59630 in GEO DataSet of NCBI database and the accession resolves in the repository. 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