Identification of Two CDK5R1-Related Subtypes and Characterization of Immune Infiltrates in Alzheimer's Disease Based on an Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36561735", "kind": "science-record", "revision": 3, "content_hash": "sha256:8a5b19a15bc33a219ac0bbc7d1ae571b2294ac2cf7374947d4ca00f610345a95", "created_at": "2026-11-01T19:01:06Z", "updated_at": "2026-11-01T22:08:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Two CDK5R1-Related Subtypes and Characterization of Immune Infiltrates in Alzheimer's Disease Based on an Integrated Bioinformatics Analysis.", "doi": "10.1155/2022/6766460", "pmid": "36561735", "authors": ["Xu Shao", "Yanxian Yang", "Jieyun Chen", "Runping Zhao", "Lei Xu", "Xilong Guo", "Yu Feng", "Lina Qin"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Background: Alzheimer's disease (AD) is a neurodegenerative disorder and the major cause of senile dementia. The Reelin pathway has been involved in both learning and AD pathogenesis. However, the specific Reelin-related gene signature during the pathological process remains unknown.\nMethods: Reelin-related gene (CDK5R1) expression was analyzed using the GEO datasets. The relevant genes of CDK5R1 were identified using differential expression analysis and weighted gene correlation network analysis (WGCNA) based on the GSE43850 dataset. ConsensusClusterPlus analysis was applied to identify subtypes (C1 and C2) of AD. The CIBERSORT algorithm was used to assess the immune cell infiltration between the two AD subtypes.\nResults: CDK5R1 was downregulated in AD. 244 differentially expressed CDK5R1-related genes (DECRGs) between the two subgroups were mainly enriched in GABAergic synapse, neuroactive ligand-receptor interaction, synapse organization, neurotransmitter transport, etc. Furthermore, the GSVA results indicated that immune-related pathways were significantly enriched in the C1 subgroup. Interestingly, 10 Reelin pathway-related genes (CRK, DAB2IP, LRP8, RELN, STAT5A, CDK5, CDK5R1, DAB1, FYN, and SH3KBP1) were abnormally expressed between the two subgroups. The proportion of T cell gamma delta, monocytes, macrophage M2, and dendritic cells activated decreased from C1 to C2, while the proportion of plasma cells, T cell follicular helper, and NK cells activated increased.\nConclusion: Two CDK5R1-related subtypes of AD were identified, helping us to better understand the role of CDK5R1 in the pathological process of AD.", "claims": [{"id": "claim-data-access", "statement": "All data in the present study can be obtained from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36561735", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "All data in the present study can be obtained from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two CDK5R1-related subtypes of AD were identified, helping us to better understand the role of CDK5R1 in the pathological process of AD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36561735", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Two CDK5R1-related subtypes of AD were identified, helping us to better understand the role of CDK5R1 in the pathological process of AD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Two CDK5R1-related subtypes of AD were identified, helping us to better understand the role of CDK5R1 in the pathological process of AD.", "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:36561735"], "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:GSE1297"], "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:GSE1297"], "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:36561735", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/6766460", "sha256": "sha256:8334c2f2ad600540f6221c310579d1f124c5eb69fe98580480a421d933d17605", "bytes": 38199, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/6766460", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9767738", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE1297", "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=GSE1297", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE1297", "version": null, "note": "All data in the present study can be obtained from the corresponding author upon reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data in the present study can be obtained from the corresponding author upon reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM21203", "GSM21204", "GSM21205", "GSM21206", "GSM21207", "GSM21208", "GSM21209", "GSM21210", "GSM21211", "GSM21212", "GSM21213", "GSM21214", "GSM21215", "GSM21216", "GSM21217", "GSM21218", "GSM21219", "GSM21220", "GSM21221", "GSM21222", "GSM21223", "GSM21224", "GSM21225", "GSM21226", "GSM21227", "GSM21228", "GSM21229", "GSM21230", "GSM21231", "GSM21232", "GSM21233"], "sample_count": 31, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Incipient Alzheimer's Disease: Microarray Correlation Analyses", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, 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