Sex Difference of Ribosome in Stroke-Induced Peripheral Immunosuppression by Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33354565", "kind": "science-record", "revision": 8, "content_hash": "sha256:eb88802e452c73f54ba8ecb1e24f3e3f876a4c83de59cb28f36972dc6c6e375d", "created_at": "2026-11-01T15:41:20Z", "updated_at": "2026-11-01T22:45:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Sex Difference of Ribosome in Stroke-Induced Peripheral Immunosuppression by Integrated Bioinformatics Analysis.", "doi": "10.1155/2020/3650935", "pmid": "33354565", "authors": ["Jian-Qin Xie", "Ya-Peng Lu", "Hong-Li Sun", "Li-Na Gao", "Pei-Pei Song", "Zhi-Jun Feng", "Chong-Ge You"], "journal": "BioMed research international", "year": 2020, "abstract": "Ischemic stroke (IS) greatly threatens human health resulting in high mortality and substantial loss of function. Recent studies have shown that the outcome of IS has sex specific, but its mechanism is still unclear. This study is aimed at identifying the sexually dimorphic to peripheral immune response in IS progression, predicting potential prognostic biomarkers that can lead to sex-specific outcome, and revealing potential treatment targets. Gene expression dataset GSE37587, including 68 peripheral whole blood samples which were collected within 24 hours from known onset of symptom and again at 24-48 hours after onset (20 women and 14 men), was downloaded from the Gene Expression Omnibus (GEO) datasets. First, using Bioconductor R package, two kinds of differentially expressed genes (DEGs) (nonsex-specific- and sex-specific-DEGs) were screened by follow-up (24-48 hours) vs. baseline (24 hours). 30 nonsex-specific DEGs (1 upregulated and 29 downregulated), 79 female-specific DEGs (25 upregulated and 54 downregulated), and none of male-specific DEGs were obtained finally. Second, bioinformatics analysis of female-specific DEGs was performed. Gene Ontology (GO) functional annotation analysis shows that DEGs were mainly enriched in translational initiation, cytosolic ribosome, and structural constituent of ribosome. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis shows that the top 6 enrichment pathways are ribosome, nuclear factor--kappa B (NF-kappa B) signaling pathway, apoptosis, mineral absorption, nonalcoholic fatty liver disease, and pertussis. Three functional modules were clustered in the protein-protein interaction (PPI) network of DEGs. The top 10 key genes of the PPI network constructed were selected, including RPS14, RPS15A, RPS24, FAU, RPL27, RPL31, RPL34, RPL35A, RSL24D1, and EEF1B2. Sex difference of ribosome in stroke-induced peripheral immunosuppression may be the potential mechanism of sex disparities in outcome after IS, and women are more likely to have stroke-induced immunosuppression. RPS14, RPS15A, RPS24, FAU, RPL27, RPL31, RPL34, RPL35A, RSL24D1, and EEF1B2 may be novel prognostic biomarkers and potential therapeutic targets for IS.", "claims": [{"id": "claim-method", "statement": "Third, the DEG analysis was performed using the Linear Models for Microarray Data (limma) package (http://www.bioconductor.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33354565", "locator": "sections[4] \"2.2. Screening for DEGs\" paragraph 2", "quote": "Third, the DEG analysis was performed using the Linear Models for Microarray Data (limma) package (http://www.bioconductor.org/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33354565", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "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:33354565"], "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:GSE37587"], "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:GSE37587"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33354565", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/3650935", "sha256": "sha256:48668861f34a86e55783256f58e2222bdc59b8fea77a47ba4bbeef0373f6ea7e", "bytes": 46256, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/3650935", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7735851", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37587", "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=GSE37587", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37587", "version": null, "note": "The data used to support the findings of this study are included within the article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are included within the article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM922887", "GSM922888", "GSM922889", "GSM922890", "GSM922891", "GSM922892", "GSM922893", "GSM922894", "GSM922895", "GSM922896", "GSM922897", "GSM922898", "GSM922899", "GSM922900", "GSM922901", "GSM922902", "GSM922903", "GSM922904", "GSM922905", "GSM922906", "GSM922907", "GSM922908", "GSM922909", "GSM922910", "GSM922911", "GSM922912", "GSM922913", "GSM922914", "GSM922915", "GSM922916", "GSM922917", "GSM922918", "GSM922919", "GSM922920", "GSM922921", "GSM922922", "GSM922923", "GSM922924", "GSM922925", "GSM922926", "GSM922927", "GSM922928", "GSM922929", "GSM922930", "GSM922931", "GSM922932", "GSM922933", "GSM922934", "GSM922935", "GSM922936", "GSM922937", "GSM922938", "GSM922939", "GSM922940", "GSM922941", "GSM922942", "GSM922943", "GSM922944", "GSM922945", "GSM922946", "GSM922947", "GSM922948", "GSM922949", "GSM922950", "GSM922951", "GSM922952", "GSM922953", "GSM922954"], "sample_count": 68, "group_sizes": null, "group_sizes_basis": null, "platform": "6883", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Ischemic Stroke at 0-24 hours and 24-48 hours after known onset of symptoms", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33354565:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdeeef1e5a397d027b44bd89366af150315df8838746217b35d16045813532f7", "bytes": 1203, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab1", "version": null, "note": "Nonsex- and sex-specific DEGs.", "structure": {"pmcid": "PMC7735851", "section_index": 13, "section_title": "3.1.1. 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Selection of Key Genes", "row_count": 11, "column_count": 5}, "table": {"label": "Table 4", "caption": "Top 10 key genes in the PPI network of the female-specific DEGs ranked by MCC method.", "rows": [["Rank", "Gene symbol", "Gene description", "MCC score", "Log2 FC"], ["1", "RPS15A", "Ribosomal protein S15a", "4354708", "-0.83625"], ["2", "RPS14", "Ribosomal protein S14", "4354704", "-0.63886"], ["3", "RPL27", "Ribosomal protein L27", "4354680", "-0.84896"], ["3", "RPL35A", "Ribosomal protein L35a", "4354680", "-0.68986"], ["5", "FAU", "FAU ubiquitin like and ribosomal protein S30 fusion", "4354584", "-0.72147"], ["5", "RPS24", "Ribosomal protein S24", "4354584", "-0.81476"], ["7", "RPL31", "Ribosomal protein L31", "4354560", "-1.0045"], ["7", "RPL34", "Ribosomal protein L34", "4354560", "-0.82663"], ["9", "EEF1B2", "Eukaryotic translation elongation factor 1 beta 2", "3991683", "-0.82928"], ["10", "RSL24D1", "Ribosomal L24 domain containing 1", "3628802", "-1.0838"]], "row_count": 11, "column_count": 5, "numeric_cells": 48, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tab4"}}], "gaps": ["asset:data:geo:GSE37587 not downloaded", "asset:data:geo:GSE37587 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": "Third, the DEG analysis was performed using the Linear Models for Microarray Data (limma) package (http://www.bioconductor.org/)."}}, {"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": "protein-protein interaction"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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. 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