Study on potential differentially expressed genes in stroke by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34313877", "kind": "science-record", "revision": 5, "content_hash": "sha256:b515ea121a755b9eb2524710931c2f5adb79926a732f8259b81a87d554e3deb4", "created_at": "2026-11-01T15:41:45Z", "updated_at": "2026-11-01T22:04:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Study on potential differentially expressed genes in stroke by bioinformatics analysis.", "doi": "10.1007/s10072-021-05470-1", "pmid": "34313877", "authors": ["Xitong Yang", "Pengyu Wang", "Shanquan Yan", "Guangming Wang"], "journal": "Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology", "year": 2022, "abstract": "Stroke is a sudden cerebrovascular circulatory disorder with high morbidity, disability, mortality, and recurrence rate, but its pathogenesis and key genes are still unclear. In this study, bioinformatics was used to deeply analyze the pathogenesis of stroke and related key genes, so as to study the potential pathogenesis of stroke and provide guidance for clinical treatment. Gene Expression profiles of GSE58294 and GSE16561 were obtained from Gene Expression Omnibus (GEO), the differentially expressed genes (DEGs) were identified between IS and normal control group. The different expression genes (DEGs) between IS and normal control group were screened with the GEO2R online tool. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the DEGs were performed. Using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and gene set enrichment analysis (GSEA), the function and pathway enrichment analysis of DEGS were performed. Then, a protein-protein interaction (PPI) network was constructed via the Search Tool for the Retrieval of Interacting Genes (STRING) database. Cytoscape with CytoHubba were used to identify the hub genes. Finally, NetworkAnalyst was used to construct the targeted microRNAs (miRNAs) of the hub genes. A total of 85 DEGs were screened out in this study, including 65 upward genes and 20 downward genes. In addition, 3 KEGG pathways, cytokine - cytokine receptor interaction, hematopoietic cell lineage, B cell receptor signaling pathway, were significantly enriched using a database for labeling, visualization, and synthetic discovery. In combination with the results of the PPI network and CytoHubba, 10 hub genes including CEACAM8, CD19, MMP9, ARG1, CKAP4, CCR7, MGAM, CD79A, CD79B, and CLEC4D were selected. Combined with DEG-miRNAs visualization, 5 miRNAs, including hsa-mir-146a-5p, hsa-mir-7-5p, hsa-mir-335-5p, and hsa-mir-27a- 3p, were predicted as possibly the key miRNAs. Our findings will contribute to identification of potential biomarkers and novel strategies for the treatment of ischemic stroke, and provide a new strategy for clinical therapy.", "claims": [{"id": "claim-method", "statement": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) was applied to perform DEGs analysis between serum samples from IS and control groups, and corrected P-value calculations to obtain |log2FC|.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34313877", "locator": "sections[6] \"Differentially expressed Gene Identification\" paragraph 2", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) was applied to perform DEGs analysis between serum samples from IS and control groups, and corrected P-value calculations to obtain |log2FC|."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34313877", "locator": "sections[20] \"notes\" paragraph 1", "quote": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites 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:34313877"], "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:GSE16561"], "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:GSE16561"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34313877", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s10072-021-05470-1", "sha256": "sha256:c61af4df6b79fb0bf5c14dc20bb7ce0ba9b7472cc56ed01c29d8eb5b0b346b67", "bytes": 31676, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s10072-021-05470-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8789718", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16561", "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=GSE16561", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16561", "version": null, "note": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM416528", "GSM416529", "GSM416530", "GSM416531", "GSM416532", "GSM416533", "GSM416534", "GSM416535", "GSM416536", "GSM416537", "GSM416538", "GSM416539", "GSM416540", "GSM416541", "GSM416542", "GSM416543", "GSM416544", "GSM416545", "GSM416546", "GSM416547", "GSM416548", "GSM416549", "GSM416550", "GSM416551", "GSM416552", "GSM416553", "GSM416554", "GSM416555", "GSM416556", "GSM416557", "GSM416558", "GSM416559", "GSM416560", "GSM416561", "GSM416562", "GSM416563", "GSM416564", "GSM416565", "GSM416566", "GSM416567", "GSM416568", "GSM416569", "GSM416570", "GSM416571", "GSM416572", "GSM416573", "GSM416574", "GSM416575", "GSM416576", "GSM416577", "GSM416578", "GSM416579", "GSM416580", "GSM416581", "GSM416582", "GSM416583", "GSM416584", "GSM416585", "GSM416586", "GSM416587", "GSM416588", "GSM416589", "GSM416590"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "6883", "taxon": "Homo sapiens", "title": "Gene expression analysis of peripheral whole blood RNA following ischemic stroke", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE58294", "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=GSE58294", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58294", "version": null, "note": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1406033", "GSM1406034", "GSM1406035", "GSM1406036", "GSM1406037", "GSM1406038", "GSM1406039", "GSM1406040", "GSM1406041", "GSM1406042", "GSM1406043", "GSM1406044", "GSM1406045", "GSM1406046", "GSM1406047", "GSM1406048", "GSM1406049", "GSM1406050", "GSM1406051", "GSM1406052", "GSM1406053", "GSM1406054", "GSM1406055", "GSM1406056", "GSM1406057", "GSM1406058", "GSM1406059", "GSM1406060", "GSM1406061", "GSM1406062", "GSM1406063", "GSM1406064", "GSM1406065", "GSM1406066", "GSM1406067", "GSM1406068", "GSM1406069", "GSM1406070", "GSM1406071", "GSM1406072", "GSM1406073", "GSM1406074", "GSM1406075", "GSM1406076", "GSM1406077", "GSM1406078", "GSM1406079", "GSM1406080", "GSM1406081", "GSM1406082", "GSM1406083", "GSM1406084", "GSM1406085", "GSM1406086", "GSM1406087", "GSM1406088", "GSM1406089", "GSM1406090", "GSM1406091", "GSM1406092", "GSM1406093", "GSM1406094", "GSM1406095", "GSM1406096", "GSM1406097", "GSM1406098", "GSM1406099", "GSM1406100", "GSM1406101", "GSM1406102", "GSM1406103", "GSM1406104", "GSM1406105", "GSM1406106", "GSM1406107", "GSM1406108", "GSM1406109", "GSM1406110", "GSM1406111", "GSM1406112", "GSM1406113", "GSM1406114", "GSM1406115", "GSM1406116", "GSM1406117", "GSM1406118", "GSM1406119", "GSM1406120", "GSM1406121", "GSM1406122", "GSM1406123", "GSM1406124"], "sample_count": 92, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Following Cardioembolic Stroke", "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:34313877:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ac1afb88c8577cb97572a00ca38fcf48ae8e53b7088bc55c4df486741d3cbc9c", "bytes": 311, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#Tab1", "version": null, "note": "Details for GEO IS data", "structure": {"pmcid": "PMC8789718", "section_index": 5, "section_title": "Microarray data", "row_count": 3, "column_count": 4}, "table": {"label": "Table 1", "caption": "Details for GEO IS data", "rows": [["Author", "Accession", "Platform", "Samples (nomal/IS sample)"], ["Barr", "GSE16561", "GPL6883", "24/39"], ["Stamova", "GSE58294", "GPL570", "23/69"]], "row_count": 3, "column_count": 4, "numeric_cells": 6, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34313877:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6956b0c90b21a014fc496890766528a60c6449e85f09321639f52dbf1348d79c", "bytes": 1686, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab2", "version": null, "note": "GO biological process terms for DEGs between the control and IS groups", "structure": {"pmcid": "PMC8789718", "section_index": 12, "section_title": "GO functional enrichment analysis and KEGG enrichment pathway", "row_count": 11, "column_count": 7}, "table": {"label": "Table 2", "caption": "GO biological process terms for DEGs between the control and IS groups", "rows": [["GOTERM_BP", "Term", "PValue", "Fold enrichment", "Count", "GeneRatio", "Genes"], ["1", "GO:0,007,165signal transduction", "0.048507425", "1.964164567", "11", "12.94117647", "CD79B, PPP4R1, IL2RB, TNFSF10, NEDD9, FLT3LG, IRS2, TNFRSF25, IQGAP1, CORO1C, SKAP2"], ["2", "GO:0,045,087innate immune response", "0.001002881", "4.339018088", "9", "10.58823529", "CLEC4D, CD6, DEFA4, MATK, HMGB2, EIF2AK2, S100A12, LY96, PADI4"], ["3", "GO:0,006,955immune response", "0.015163648", "3.44693704", "7", "8.235294118", "CD79B, NFIL3, IL1R2, TNFSF10, CCR7, TNFRSF25, CEACAM8"], ["4", "GO:0,006,468protein phosphorylation", "0.02156091", "3.182369504", "7", "8.235294118", "PPP4R1, TAOK1, MATK, PDK4, EIF2AK2, IRAK3, PASK"], ["5", "GO:0,032,496response to lipopolysaccharide", "0.001113916", "7.584462511", "6", "7.058823529", "CD6, HMGB2, LY96, CCR7, IRAK3, TNFRSF25"], ["6", "GO:0,006,954inflammatory response", "0.034625375", "3.281931008", "6", "7.058823529", "TPST1, ORM1, S100A12, LY96, CCR7, TNFRSF25"], ["7", "GO:0,007,166cell surface receptor signaling pathway", "0.041831035", "3.783004416", "5", "5.882352941", "CD19, TNFSF10, LY96, EVL, TNFRSF25"], ["8", "GO:0,050,853B cell receptor signaling pathway", "0.002168409", "15.3561957", "4", "4.705882353", "CD79B, CD79A, PLEKHA1, CD19"], ["9", "GO:0,002,250adaptive immune response", "0.033682623", "5.60293627", "4", "4.705882353", "CD79B, CD79A, CLEC4D, CD6"], ["10", "GO:0,071,345cellular response to cytokine stimulus", "0.004867389", "28.26936027", "3", "3.529411765", "MME, LEF1, CCR7"]], "row_count": 11, "column_count": 7, "numeric_cells": 68, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34313877:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:de28c488a046467e693ecc15caf857147cc17f1b42e5559c8e4cd3bf04c83918", "bytes": 1471, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#Tab3", "version": null, "note": "GO molecular function terms for DEGs between the control and IS groups", "structure": {"pmcid": "PMC8789718", "section_index": 12, "section_title": "GO functional enrichment analysis and KEGG enrichment pathway", "row_count": 11, "column_count": 7}, "table": {"label": "Table 3", "caption": "GO molecular function terms for DEGs between the control and IS groups", "rows": [["GOTERM_MF", "Term", "PValue", "Fold enrichment", "Count", "GeneRatio", "Genes"], ["1", "GO:0,005,509calcium ion binding", "0.018741709", "2.648692469", "9", "10.58823529", "NELL2, ANXA3, REPS2, DYSF, S100A12, ITPR3, PADI4, IQGAP1, DSC2"], ["2", "GO:0,019,904protein domain-specific binding", "0.016406406", "5.072415865", "5", "5.882352941", "LAMP2, HMGB2, ID3, IRS2, IQGAP1"], ["3", "GO:0,016,301kinase activity", "0.026474471", "4.377852697", "5", "5.882352941", "NELL2, PRKAR1A, TAOK1, PDK4, FLT3LG"], ["4", "GO:0,005,102receptor binding", "0.083617609", "2.988845609", "5", "5.882352941", "ABCA1, ACOX1, MATK, TNFSF10, FLT3LG"], ["5", "GO:0,003,824catalytic activity", "0.058139482", "4.48962766", "4", "4.705882353", "HAL, MGAM, ACSL1, ECHDC3"], ["6", "GO:0,003,714transcription corepressor activity", "0.069792981", "4.157881773", "4", "4.705882353", "NFIL3, ID3, SAP30, AES"], ["7", "GO:0,030,165PDZ domain binding", "0.061420984", "7.360901163", "3", "3.529411765", "SLC22A4, PLEKHA1, ACOX1"], ["8", "GO:0,005,522profilin binding", "0.041348098", "46.89166667", "2", "2.352941176", "VASP, EVL"], ["9", "GO:0,050,786RAGE receptor binding", "0.050304763", "38.36590909", "2", "2.352941176", "HMGB2, S100A12"], ["10", "GO:0,008,301DNA binding, bending", "0.081007285", "23.44583333", "2", "2.352941176", "LEF1, HMGB2"]], "row_count": 11, "column_count": 7, "numeric_cells": 65, "header_rows": 1, "locator": "section[12]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:34313877:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:16b6623b51c58ea7f1c02a73b21ed66534fcae3e3f029f120601d184a1df9e47", "bytes": 2387, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[3]#Tab4", "version": null, "note": "GO cellular component terms for DEGs between the control and IS group", "structure": {"pmcid": "PMC8789718", "section_index": 12, "section_title": "GO functional enrichment analysis and KEGG enrichment pathway", "row_count": 11, "column_count": 7}, "table": {"label": "Table 4", "caption": "GO cellular component terms for DEGs between the control and IS group", "rows": [["GOTERM_CC", "Term", "P value", "Fold enrichment", "Count", "GeneRatio", "Genes"], ["1", "GO:0,005,886plasma membrane", "5.44E-05", "1.895240406", "36", "42.35294118", "SLC22A4, SNAP23, DYSF, LY96, IRS2, ITPR3, IQGAP1, CD79B, CD79A, CD19, LAMP2, CA4, S100A12, CCR7, ABCA1, VASP, SVIL, MGAM, CD163, PLEKHA1, MME, ACSL1, ANXA3, IL1R2, KCNJ15, CKAP4, MARCKS, CLEC4D, ACOX1, VNN3, CPD, IL2RB, TNFRSF25, CEACAM8, DSC2, SKAP2"], ["2", "GO:0,005,737cytoplasm", "0.08417535", "1.287921067", "31", "36.47058824", "SNAP23, LEF1, HMGB2, NEDD9, ITPR3, ABHD5, IQGAP1, CORO1C, CD79B, CD79A, REPS2, S100A12, VASP, SVIL, PLEKHA1, MME, ANXA3, ARG1, IL1R2, EIF2AK2, IRAK3, PASK, RBP7, PRKAR1A, TAOK1, DPYD, ID3, EVL, PADI4, GRAP, SKAP2"], ["3", "GO:0,070,062extracellular exosome", "5.30E-04", "2.006674459", "26", "30.58823529", "ORM1, SNAP23, DYSF, IQGAP1, CD79B, CD19, LAMP2, CA4, TNFSF10, VASP, MGAM, PLEKHA1, MME, ANXA3, ARG1, PLXDC2, MMP9, CKAP4, RAB33B, MARCKS, CRISPLD2, TAOK1, CPD, CEACAM8, MFGE8, DSC2"], ["4", "GO:0,016,020membrane", "0.001726377", "2.070909091", "21", "24.70588235", "CD163, ACSL1, ANXA3, DOCK8, KCNJ15, EIF2AK2, FLT3LG, ITPR3, CKAP4, HK2, TPST1, CD6, PRKAR1A, ACOX1, CPD, IL2RB, LAMP2, CA4, EVL, FOLR3, MFGE8"], ["5", "GO:0,005,887integral component of plasma membrane", "0.011315379", "2.146525324", "14", "16.47058824", "ABCA1, SLC22A4, CD163, MME, KCNJ15, ITPR3, CD79B, CD79A, CD6, CD19, IL2RB, TNFSF10, TNFRSF25, CEACAM8"], ["6", "GO:0,005,576extracellular region", "0.029681411", "1.886542443", "14", "16.47058824", "ORM1, CD163, DEFA4, IL1R2, FLT3LG, MMP9, NELL2, CD6, CRISPLD2, TNFSF10, S100A12, TNFRSF25, FOLR3, MFGE8"], ["7", "GO:0,005,615extracellular space", "0.018583106", "2.093824018", "13", "15.29411765", "ORM1, ARG1, DEFA4, HMGB2, FLT3LG, LY96, MMP9, VNN3, CPD, LAMP2, TNFSF10, CEACAM8, MFGE8"], ["8", "GO:0,005,925focal adhesion", "4.05E-04", "4.99378882", "9", "10.58823529", "VASP, SVIL, MARCKS, MME, SNAP23, NEDD9, EVL, IQGAP1, CORO1C"], ["9", "GO:0,009,897external side of plasma membrane", "4.24E-04", "7.129890454", "7", "8.235294118", "ABCA1, CD79B, CD79A, CD19, IL2RB, CCR7, MFGE8"], ["10", "GO:0,030,027lamellipodium", "0.006143732", "6.779761905", "5", "5.882352941", "VASP, DYSF, NEDD9, EVL, CORO1C"]], "row_count": 11, "column_count": 7, "numeric_cells": 69, "header_rows": 1, "locator": "section[12]/table-wrap[3]#Tab4"}}, {"id": "asset:table:pmid:34313877:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3ff0ba6d98ecb18dd84f0f793442b62105602ccbe8c9aec2c9786e6a253e31ee", "bytes": 673, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[4]#Tab5", "version": null, "note": "KEGG pathway enrichment terms for DEGs between the control and IS group", "structure": {"pmcid": "PMC8789718", "section_index": 12, "section_title": "GO functional enrichment analysis and KEGG enrichment pathway", "row_count": 4, "column_count": 7}, "table": {"label": "Table 5", "caption": "KEGG pathway enrichment terms for DEGs between the control and IS group", "rows": [["KEGG_pathway", "Term", "PValue", "Fold enrichment", "Count", "GeneRatio", "Genes"], ["1", "hsa04060Cytokine-cytokine receptor interaction", "0.059651063", "3.291702555", "5", "5.882352941", "IL1R2, IL2RB, TNFSF10, CCR7, TNFRSF25"], ["2", "hsa04640Hematopoietic cell lineage", "0.01572673", "7.355252606", "4", "4.705882353", "MME, CD19, IL1R2, FLT3LG"], ["3", "hsa04662B cell receptor signaling pathway", "0.066036489", "6.955510617", "3", "3.529411765", "CD79B, CD79A, CD19"]], "row_count": 4, "column_count": 7, "numeric_cells": 21, "header_rows": 1, "locator": "section[12]/table-wrap[4]#Tab5"}}], "gaps": ["asset:data:geo:GSE16561 not downloaded", "asset:data:geo:GSE16561 licence not read", "asset:data:geo:GSE58294 not downloaded", "asset:data:geo:GSE58294 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "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"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R differential expression analysis using corrected P-value calculations and |log2FC| thresholds", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r) was applied to perform DEGs analysis between serum samples from IS and control groups, and corrected P-value calculations to obtain |log2FC|."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE58294", "GSE16561"], "resolved_accessions": ["GSE58294", "GSE16561"], "statements": ["The data used in this study were downloaded from the GEO database. The data used to support the findings of this study are available from corresponding websites upon request."], "basis": "The paper names GSE58294, GSE16561 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34313877", "data:geo:GSE16561", "asset:table:pmid:34313877:1", "asset:table:pmid:34313877:2", "asset:table:pmid:34313877:3", "asset:table:pmid:34313877:4", "asset:table:pmid:34313877:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16561"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25396, "completion_tokens": 1625, "cached_tokens": 776}}, "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:34313877", "type": "paper", "label": "pmid:34313877"}, {"id": "source:pmid:34313877", "type": "manuscript", "label": "PMID 34313877 full text"}, {"id": "data:geo:GSE16561", "type": "dataset", "label": "GEO GSE16561"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34313877", "type": "paper", "label": "pmid:34313877"}, {"id": "source:pmid:34313877", "type": "manuscript", "label": "PMID 34313877 full text"}, {"id": "data:geo:GSE16561", "type": "dataset", "label": "GEO GSE16561"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34313877", "type": "extraction", "used": ["source:pmid:34313877"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16561", "type": "accession_resolution", "used": ["data:geo:GSE16561"], "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:34313877", "parent_hash": "sha256:1c2c56d4a2da57320bc4cd17129bf8c53d7156d908f473c14c1ae1f9f9753dba", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE16561 licence not read", "asset:data:geo:GSE16561 not downloaded", "asset:data:geo:GSE58294 licence not read", "asset:data:geo:GSE58294 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}