Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31183363", "kind": "science-record", "revision": 8, "content_hash": "sha256:28373ebf61c4ee2c395a08eae5eed6782c1683f8984eea281d1578d5d838b7a7", "created_at": "2026-11-01T15:40:45Z", "updated_at": "2026-11-01T22:44:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke.", "doi": "10.1155/2019/2478453", "pmid": "31183363", "authors": ["Wenhao Zhu", "Yinan Nan", "Shaoqing Wang", "Wei Liu"], "journal": "BioMed research international", "year": 2019, "abstract": "Ischemic stroke (IS) is a complex disease with sex differences in epidemiology, presentations, and outcomes. However, the sex-specific mechanism underlying IS remains unclear. The purpose of this study was to identify key genes contributing to biological differences between sexes. First, we downloaded the gene expression data of GSE22255 from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using R software and related packages. Second, DEGs were separately analyzed by Gene Ontology enrichment and pathways analyses. Third, protein-protein interaction (PPI) network was constructed to further investigate the interactions of DEGs. A total of 123 DEGs were identified between sexes, including 8 upregulated and 115 downregulated genes. In the PPI network, ten key genes were identified, including IL1α, IL1β, IL6, IL8, CXCL1, CXCL2, CXCL20, CCL4, ICAM1, and PTGS2. Functional enrichment analysis revealed that these genes were mainly enriched in biological processes of immune response and apoptotic process, also in pathways of TNF and NOD-like receptor signaling. In conclusion, the above ten genes may have a protective effect on IS females through their direct or indirect involvement in biological processes of immune response and apoptotic process, as well as in TNF and NOD-like receptor signaling pathways. The results of this study may help to gain new insights into the sex-specific mechanisms underlying IS females and may suggest potential therapeutic targets for disease treatment.", "claims": [{"id": "claim-method", "statement": "Then, DEGs between IS females and males were screened by Linear Models for Microarray Data (limma) package in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31183363", "locator": "sections[4] \"2.2. Differential Expression Analysis\" paragraph 2", "quote": "Then, DEGs between IS females and males were screened by Linear Models for Microarray Data (limma) package in R."}], "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:31183363", "locator": "sections[14] \"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:31183363"], "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:GSE22255"], "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:GSE22255"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31183363", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2019/2478453", "sha256": "sha256:f4bcbb35bfcf7556d684021f31326478c1206d50fb57e04b5d1c12d759ebb010", "bytes": 21368, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2019/2478453", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6515108", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22255", "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=GSE22255", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22255", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM554014", "GSM554015", "GSM554016", "GSM554017", "GSM554018", "GSM554019", "GSM554020", "GSM554021", "GSM554022", "GSM554023", "GSM554024", "GSM554025", "GSM554026", "GSM554027", "GSM554028", "GSM554029", "GSM554030", "GSM554031", "GSM554032", "GSM554033", "GSM554034", "GSM554035", "GSM554036", "GSM554037", "GSM554038", "GSM554039", "GSM554040", "GSM554041", "GSM554042", "GSM554043", "GSM554044", "GSM554045", "GSM554046", "GSM554047", "GSM554048", "GSM554049", "GSM554050", "GSM554051", "GSM554052", "GSM554053"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Blood genomic expression profile for ischemic stroke (IS)", "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:31183363:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:989a09aca9948aa2a43cfad3a09c94e1314dbecc4fe599138abc746dd4125323", "bytes": 1178, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#tab1", "version": null, "note": "Top 8 up- and 10 downregulated differentially expressed genes of ischemic stroke in women versus men.", "structure": {"pmcid": "PMC6515108", "section_index": 8, "section_title": "3.1. Identification of DEGs", "row_count": 19, "column_count": 5}, "table": {"label": "Table 1", "caption": "Top 8 up- and 10 downregulated differentially expressed genes of ischemic stroke in women versus men.", "rows": [["Gene ID", "Gene symbol", "Adj. p value", "logFC", "Up- or downregulation"], ["224588_at", "XIST", "9.54E-23", "8.47", "Up"], ["206207_at", "CLC", "2.54E-17", "5.09", "Up"], ["231592_at", "TSIX", "7.49E-06", "2.18", "Up"], ["204069_at", "MEIS1", "2.26 E-03", "1.77", "Up"], ["228195_at", "C2orf88", "6.96 E-03", "1.68", "Up"], ["209930_s_at", "NFE2", "7.56 E-03", "1.62", "Up"], ["1559477_s_at", "MEIS1", "1.40 E-03", "1.60", "Up"], ["223377_x_at", "CISH", "2.21 E-03", "1.59", "Up"], ["201909_at", "RPS4Y1", "2.76E-23", "-7.46", "Down"], ["205000_at", "DDX3Y", "1.45E-19", "-7.24", "Down"], ["204470_at", "CXCL1", "4.96E-21", "-5.84", "Down"], ["207850_at", "CXCL4", "8.97 E-03", "-5.15", "Down"], ["39402_at", "IL1β", "7.11E-14", "-5.01", "Down"], ["210118_s_at", "IL1α", "8.14 E-04", "-4.75", "Down"], ["205476_at", "CCL20", "1.536 E-03", "-4.64", "Down"], ["1569203_at", "CXCL2", "6.72E-13", "-4.53", "Down"], ["205207_at", "IL6", "3.60 E-03", "-4.26", "Down"], ["228492_at", "USP9Y", "4.22E-21", "-4.08", "Down"]], "row_count": 19, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tab1"}}], "gaps": ["asset:data:geo:GSE22255 not downloaded", "asset:data:geo:GSE22255 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": "Then, DEGs between IS females and males were screened by Linear Models for Microarray Data (limma) package in R."}}, {"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"}}], "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": ["GSE22255"], "resolved_accessions": ["GSE22255"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE22255 in 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:31183363", "data:geo:GSE22255", "asset:table:pmid:31183363:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22255"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18381, "completion_tokens": 905, "cached_tokens": 6280}}, "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:31183363", "type": "paper", "label": "pmid:31183363"}, {"id": "source:pmid:31183363", "type": "manuscript", "label": "PMID 31183363 full text"}, {"id": "data:geo:GSE22255", "type": "dataset", "label": "GEO GSE22255"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31183363", "type": "paper", "label": "pmid:31183363"}, {"id": "source:pmid:31183363", "type": "manuscript", "label": "PMID 31183363 full text"}, {"id": "data:geo:GSE22255", "type": "dataset", "label": "GEO GSE22255"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31183363", "type": "extraction", "used": ["source:pmid:31183363"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22255", "type": "accession_resolution", "used": ["data:geo:GSE22255"], "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:31183363", "parent_hash": "sha256:89251d376e3674c9540071f4061f961e0e6be4eeb2ef1cd215a9f343ff3d72c0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE22255 licence not read", "asset:data:geo:GSE22255 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": ["Then, DEGs between IS females and males were screened by Linear Models for Microarray Data (limma) package in R."], "order_basis": "analysis_only", "id": "assay:1"}]}