The potential crosstalk genes and molecular mechanisms between glioblastoma and periodontitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38472293", "kind": "science-record", "revision": 4, "content_hash": "sha256:0aa1e94e4b273490e47345a6aaef8989aa67ccaaa21428d964b8a25b783bff2a", "created_at": "2026-11-01T19:20:25Z", "updated_at": "2026-11-01T22:11:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The potential crosstalk genes and molecular mechanisms between glioblastoma and periodontitis.", "doi": "10.1038/s41598-024-56577-2", "pmid": "38472293", "authors": ["Jian-Huang Huang", "Yao Chen", "Yuan-Bao Kang", "Zheng-Jian Yao", "Jian-Hua Song"], "journal": "Scientific reports", "year": 2024, "abstract": "Despite clinical and epidemiological evidence suggestive of a link between glioblastoma (GBM) and periodontitis (PD), the shared mechanisms of gene regulation remain elusive. In this study, we identify differentially expressed genes (DEGs) that overlap between the GEO datasets GSE4290 [GBM] and GSE10334 [PD]. Functional enrichment analysis was conducted, and key modules were identified using protein-protein interaction (PPI) network and weighted gene co-expression network analysis (WGCNA). The expression levels of CXCR4, LY96, and C3 were found to be significantly elevated in both the test dataset and external validation dataset, making them key crosstalk genes. Additionally, immune cell landscape analysis revealed elevated expression levels of multiple immune cells in GBM and PD compared to controls, with the key crosstalk genes negatively associated with Macrophages M2. FLI1 was identified as a potential key transcription factor (TF) regulating the three key crosstalk genes, with increased expression in the full dataset. These findings contribute to our understanding of the immune and inflammatory aspects of the comorbidity mechanism between GBM and PD.", "claims": [{"id": "claim-method", "statement": "Subsequently, we identified three crosstalk genes (CXCR4, LY96, and C3) in GBM and PD using a combined screen of PPI network, hub genes, and WGCNA analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38472293", "locator": "sections[21] \"Discussion\" paragraph 6", "quote": "Subsequently, we identified three crosstalk genes (CXCR4, LY96, and C3) in GBM and PD using a combined screen of PPI network, hub genes, and WGCNA analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38472293", "locator": "sections[28] \"notes\" paragraph 1", "quote": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The expression levels of CXCR4, LY96, and C3 were found to be significantly elevated in both the test dataset and external validation dataset, making them key crosstalk genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38472293", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The expression levels of CXCR4, LY96, and C3 were found to be significantly elevated in both the test dataset and external validation dataset, making them key crosstalk genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The expression levels of CXCR4, LY96, and C3 were found to be significantly elevated in both the test dataset and external validation dataset, making them key crosstalk genes.", "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:38472293"], "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:GSE10334"], "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:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38472293", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-56577-2", "sha256": "sha256:12d47902fca6114b02c9133f77ebba1565941ce772291e6c3a89771044e6ef70", "bytes": 31594, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-56577-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10933479", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10334", "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=GSE10334", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10334", "version": null, "note": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM261086", "GSM261087", "GSM261088", "GSM261089", "GSM261090", "GSM261091", "GSM261092", "GSM261093", "GSM261094", "GSM261095", "GSM261096", "GSM261097", "GSM261098", "GSM261099", "GSM261100", "GSM261101", "GSM261102", "GSM261103", "GSM261104", "GSM261105", "GSM261106", "GSM261107", "GSM261108", "GSM261109", "GSM261110", "GSM261111", "GSM261112", "GSM261113", "GSM261114", "GSM261115", "GSM261116", "GSM261117", "GSM261118", "GSM261119", "GSM261120", "GSM261121", "GSM261122", "GSM261123", "GSM261124", "GSM261125", "GSM261126", "GSM261127", "GSM261128", "GSM261129", "GSM261130", "GSM261131", "GSM261132", "GSM261133", "GSM261134", "GSM261135", "GSM261136", "GSM261137", "GSM261138", "GSM261139", "GSM261140", "GSM261141", "GSM261142", "GSM261143", "GSM261144", "GSM261145", "GSM261146", "GSM261147", "GSM261148", "GSM261149", "GSM261150", "GSM261151", "GSM261152", "GSM261153", "GSM261154", "GSM261155", "GSM261156", "GSM261157", "GSM261158", "GSM261159", "GSM261160", "GSM261161", "GSM261162", "GSM261163", "GSM261164", "GSM261165", "GSM261166", "GSM261167", "GSM261168", "GSM261169", "GSM261170", "GSM261171", "GSM261172", "GSM261173", "GSM261174", "GSM261175", "GSM261176", "GSM261177", "GSM261178", "GSM261179", "GSM261180", "GSM261181", "GSM261182", "GSM261183", "GSM261184", "GSM261185", "GSM261186", "GSM261187", "GSM261188", "GSM261189", "GSM261190", "GSM261191", "GSM261192", "GSM261193", "GSM261194", "GSM261195", "GSM261196", "GSM261197", "GSM261198", "GSM261199", "GSM261200", "GSM261201", "GSM261202", "GSM261203", "GSM261204", "GSM261205", "GSM261206", "GSM261207", "GSM261208", "GSM261209", "GSM261210", "GSM261211", "GSM261212", "GSM261213", "GSM261214", "GSM261215", "GSM261216", "GSM261217", "GSM261218", "GSM261219", "GSM261220", "GSM261221", "GSM261222", "GSM261223", "GSM261224", "GSM261225", "GSM261226", "GSM261227", "GSM261228", "GSM261229", "GSM261230", "GSM261231", "GSM261232", "GSM261233", "GSM261234", "GSM261235", "GSM261236", "GSM261237", "GSM261238", "GSM261239", "GSM261240", "GSM261241", "GSM261242", "GSM261243", "GSM261244", "GSM261245", "GSM261246", "GSM261247", "GSM261248", "GSM261249", "GSM261250", "GSM261251", "GSM261252", "GSM261253", "GSM261254", "GSM261255", "GSM261256", "GSM261257", "GSM261258", "GSM261259", "GSM261260", "GSM261261", "GSM261262", "GSM261263", "GSM261264", "GSM261265", "GSM261266", "GSM261267", "GSM261268", "GSM261269", "GSM261270", "GSM261271", "GSM261272", "GSM261273", "GSM261274", "GSM261275", "GSM261276", "GSM261277", "GSM261278", "GSM261279", "GSM261280", "GSM261281", "GSM261282", "GSM261283", "GSM261284", "GSM261285", "GSM261286", "GSM261287", "GSM261288", "GSM261289", "GSM261290", "GSM261291", "GSM261292", "GSM261293", "GSM261294", "GSM261295", "GSM261296", "GSM261297", "GSM261298", "GSM261299", "GSM261300", "GSM261301", "GSM261302", "GSM261303", "GSM261304", "GSM261305", "GSM261306", "GSM261307", "GSM261308", "GSM261309", "GSM261310", "GSM261311", "GSM261312", "GSM261313", "GSM261314", "GSM261315", "GSM261316", "GSM261317", "GSM261318", "GSM261319", "GSM261320", "GSM261321", "GSM261322", "GSM261323", "GSM261324", "GSM261325", "GSM261326", "GSM261327", "GSM261328", "GSM261329", "GSM261330", "GSM261331", "GSM261332"], "sample_count": 247, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptomes in Healthy and Diseased Gingival Tissues", "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:GSE12657", "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=GSE12657", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12657", "version": null, "note": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM317711", "GSM317712", "GSM317713", "GSM317714", "GSM317715", "GSM317716", "GSM317717", "GSM317718", "GSM317719", "GSM317720", "GSM317721", "GSM317722", "GSM317723", "GSM317724", "GSM317725", "GSM317726", "GSM317727", "GSM317728", "GSM317729", "GSM317730", "GSM317731", "GSM317732", "GSM317733", "GSM317734", "GSM317735"], "sample_count": 25, "group_sizes": null, "group_sizes_basis": null, "platform": "8300", "taxon": "Homo sapiens", "title": "Expression data from human glioma samples", "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:GSE14805", "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=GSE14805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14805", "version": null, "note": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM370578", "GSM370579", "GSM370580", "GSM370581", "GSM370582", "GSM370583", "GSM370584", "GSM370585", "GSM370586", "GSM370587", "GSM370588", "GSM370589", "GSM370590", "GSM370591", "GSM370592", "GSM370593", "GSM370594", "GSM370595", "GSM370596", "GSM370597", "GSM370598", "GSM370599", "GSM370600", "GSM370601", "GSM370602", "GSM370603", "GSM370604", "GSM370605", "GSM370606", "GSM370607", "GSM370608", "GSM370609", "GSM370610", "GSM370611", "GSM370612", "GSM370613", "GSM370614", "GSM370615"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "3921", "taxon": "Homo sapiens", "title": "Transcript expression data from glioblastoma subcutaneous xenografts and non-neoplastic control brain", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE16134", "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=GSE16134", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16134", "version": null, "note": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM404005", "GSM404006", "GSM404007", "GSM404008", "GSM404009", "GSM404010", "GSM404011", "GSM404012", "GSM404013", "GSM404014", "GSM404015", "GSM404016", "GSM404017", "GSM404018", "GSM404019", "GSM404020", "GSM404021", "GSM404022", "GSM404023", "GSM404024", "GSM404025", "GSM404026", "GSM404027", "GSM404028", "GSM404029", "GSM404030", "GSM404031", "GSM404032", "GSM404033", "GSM404034", "GSM404035", "GSM404036", "GSM404037", "GSM404038", "GSM404039", "GSM404040", "GSM404041", "GSM404042", "GSM404043", "GSM404044", "GSM404045", "GSM404046", "GSM404047", "GSM404048", "GSM404049", "GSM404050", "GSM404051", "GSM404052", "GSM404053", "GSM404054", "GSM404055", "GSM404056", "GSM404057", "GSM404058", "GSM404059", "GSM404060", "GSM404061", "GSM404062", "GSM404063", 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"GSM404295", "GSM404296", "GSM404297", "GSM404298", "GSM404299", "GSM404300", "GSM404301", "GSM404302", "GSM404303", "GSM404304", "GSM404305", "GSM404306", "GSM404307", "GSM404308", "GSM404309", "GSM404310", "GSM404311", "GSM404312", "GSM404313", "GSM404314"], "sample_count": 310, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Bacterial Correlates of Gingival Gene Expression", "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:GSE4290", "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=GSE4290", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4290", "version": null, "note": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM97793", "GSM97794", "GSM97795", "GSM97796", "GSM97797", "GSM97798", "GSM97799", "GSM97800", "GSM97801", "GSM97802", "GSM97803", "GSM97804", "GSM97805", "GSM97806", "GSM97807", "GSM97808", "GSM97809", "GSM97810", "GSM97811", "GSM97812", "GSM97813", "GSM97814", "GSM97815", "GSM97816", "GSM97817", "GSM97818", "GSM97819", "GSM97820", "GSM97821", "GSM97822", "GSM97823", "GSM97824", "GSM97825", "GSM97826", "GSM97827", "GSM97828", "GSM97829", "GSM97830", "GSM97831", "GSM97832", "GSM97833", "GSM97834", "GSM97835", "GSM97836", "GSM97837", "GSM97838", "GSM97839", "GSM97840", "GSM97841", "GSM97842", "GSM97843", "GSM97844", "GSM97845", "GSM97846", "GSM97847", "GSM97848", "GSM97849", "GSM97850", "GSM97851", "GSM97852", "GSM97853", "GSM97854", "GSM97855", "GSM97856", "GSM97857", "GSM97858", "GSM97859", "GSM97860", "GSM97861", "GSM97862", "GSM97863", "GSM97864", "GSM97865", "GSM97866", "GSM97867", "GSM97868", "GSM97869", "GSM97870", "GSM97871", "GSM97872", "GSM97873", "GSM97874", "GSM97875", "GSM97876", "GSM97877", "GSM97878", "GSM97879", "GSM97880", "GSM97881", "GSM97882", "GSM97883", "GSM97884", "GSM97885", "GSM97886", "GSM97887", "GSM97888", "GSM97889", "GSM97890", "GSM97891", "GSM97892", "GSM97893", "GSM97894", "GSM97895", "GSM97896", "GSM97897", "GSM97898", "GSM97899", "GSM97900", "GSM97901", "GSM97902", "GSM97903", "GSM97904", "GSM97905", "GSM97906", "GSM97907", "GSM97908", "GSM97909", "GSM97910", "GSM97911", "GSM97912", "GSM97913", "GSM97914", "GSM97915", "GSM97916", "GSM97917", "GSM97918", "GSM97919", "GSM97920", "GSM97921", "GSM97922", "GSM97923", "GSM97924", "GSM97925", "GSM97926", "GSM97927", "GSM97928", "GSM97929", "GSM97930", "GSM97931", "GSM97932", "GSM97933", "GSM97934", "GSM97935", "GSM97936", "GSM97937", "GSM97938", "GSM97939", "GSM97940", "GSM97941", "GSM97942", "GSM97943", "GSM97944", "GSM97945", "GSM97946", "GSM97947", "GSM97948", "GSM97949", "GSM97950", "GSM97951", "GSM97952", "GSM97953", "GSM97954", "GSM97955", "GSM97956", "GSM97957", "GSM97958", "GSM97959", "GSM97960", "GSM97961", "GSM97962", "GSM97963", "GSM97964", "GSM97965", "GSM97966", "GSM97967", "GSM97968", "GSM97969", "GSM97970", "GSM97971", "GSM97972"], "sample_count": 180, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data of glioma samples from Henry Ford Hospital", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10334 not downloaded", "asset:data:geo:GSE10334 licence not read", "asset:data:geo:GSE12657 not downloaded", "asset:data:geo:GSE12657 licence not read", "asset:data:geo:GSE14805 not downloaded", "asset:data:geo:GSE14805 licence not read", "asset:data:geo:GSE16134 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE4290 not downloaded", "asset:data:geo:GSE4290 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "verbatim", "quote": "Subsequently, we identified three crosstalk genes (CXCR4, LY96, and C3) in GBM and PD using a combined screen of PPI network, hub genes, and WGCNA analysis."}}], "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": ["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": ["GSE4290", "GSE10334", "GSE14805", "GSE16134", "GSE12657"], "resolved_accessions": ["GSE4290", "GSE10334", "GSE14805", "GSE16134", "GSE12657"], "statements": ["Data availabilityThe datasets analyzed in this study are available for download in the Gene Expression Omnibus (GEO) and TCGA-GBM dataset. GSE4290dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4290. GSE10334 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10334. GSE12657 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12657. GSE16134 dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16134. TCGA-GBM dataset: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Glioblastoma%20(GBM)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443."], "basis": "The paper names GSE4290, GSE10334, GSE14805, GSE16134, GSE12657 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:38472293", "data:geo:GSE10334"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10334"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:11:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9056, "completion_tokens": 3512, "cached_tokens": 188}}, "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:38472293", "type": "paper", "label": "pmid:38472293"}, {"id": "source:pmid:38472293", "type": "manuscript", "label": "PMID 38472293 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38472293", "type": "paper", "label": "pmid:38472293"}, {"id": "source:pmid:38472293", "type": "manuscript", "label": "PMID 38472293 full text"}, {"id": "data:geo:GSE10334", "type": "dataset", "label": "GEO GSE10334"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38472293", "type": "extraction", "used": ["source:pmid:38472293"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10334", "type": "accession_resolution", "used": ["data:geo:GSE10334"], "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:38472293", "parent_hash": "sha256:e1bd16736adbd577f11fa05daa43dfc1055b80e00b58337a2e78cbf16239004c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE10334 licence not read", "asset:data:geo:GSE10334 not downloaded", "asset:data:geo:GSE12657 licence not read", "asset:data:geo:GSE12657 not downloaded", "asset:data:geo:GSE14805 licence not read", "asset:data:geo:GSE14805 not downloaded", "asset:data:geo:GSE16134 licence not read", "asset:data:geo:GSE16134 not downloaded", "asset:data:geo:GSE4290 licence not read", "asset:data:geo:GSE4290 not downloaded", "execution.not_run", "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": 1.0, "evidence": ["Subsequently, we identified three crosstalk genes (CXCR4, LY96, and C3) in GBM and PD using a combined screen of PPI network, hub genes, and WGCNA analysis."], "order_basis": "analysis_only", "id": "assay:1"}]}