Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32210915", "kind": "science-record", "revision": 7, "content_hash": "sha256:4543eac9dab9ebacd4b2958ba76def96c251428a9cdb982d25165b8cf1b32434", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T22:01:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome.", "doi": "10.3389/fendo.2020.00104", "pmid": "32210915", "authors": ["Hao Wang", "Hui Zhu", "Wenjiao Zhu", "Yue Xu", "Nan Wang", "Bing Han", "Huaidong Song", "Jie Qiao"], "journal": "Frontiers in endocrinology", "year": 2020, "abstract": "Background: Turner syndrome (TS) is a sex chromosome aneuploidy with a variable spectrum of symptoms including short stature, ovarian failure and skeletal abnormalities. The etiology of TS is complex, and the mechanisms driving its pathogenesis remain unclear. Methods: In our study, we used the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE46687 to identify differentially expressed genes (DEGs) between monosomy X TS patients and normal female individuals. The relevant data on 26 subjects with TS (45,XO) and 10 subjects with the normal karyotype (46,XX) was investigated. Then, tissue-specific gene expression, functional enrichment, and protein-protein interaction (PPI) network analyses were performed, and the key modules were identified. Results: In total, 25 upregulated and 60 downregulated genes were identified in the differential expression analysis. The tissue-specific gene expression analysis of the DEGs revealed that the system with the most highly enriched tissue-specific gene expression was the hematologic/immune system, followed by the skin/skeletal muscle and neurologic systems. The PPI network analysis, construction of key modules and manual screening of tissue-specific gene expression resulted in the identification of the following five genes of interest: CD99, CSF2RA, MYL9, MYLPF, and IGFBP2. CD99 and CSF2RA are involved in the hematologic/immune system, MYL9 and MYLPF are related to the circulatory system, and IGFBP2 is related to skeletal abnormalities. In addition, several genes of interest with possible roles in the pathogenesis of TS were identified as being associated with the hematologic/immune system or metabolism. Conclusion: This discovery-driven analysis may be a useful method for elucidating novel mechanisms underlying TS. However, more experiments are needed to further explore the relationships between these genes and TS in the future.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed using the online analysis tool GEO2R; the expression profiles of monosomy X TS patients and normal 46,XX females were compared to identify the DEGs. P-values and adjusted P-values were calculated using t-tests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32210915", "locator": "sections[4] \"Differential Expression Analysis\" paragraph 2", "quote": "Differential expression analysis was performed using the online analysis tool GEO2R; the expression profiles of monosomy X TS patients and normal 46,XX females were compared to identify the DEGs. P-values and adjusted P-values were calculated using t-tests."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in the GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46687, using code GSE46687.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32210915", "locator": "sections[15] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated for this study can be found in the GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46687, using code GSE46687."}], "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:32210915"], "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:GSE46687"], "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:GSE46687"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32210915", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fendo.2020.00104", "sha256": "sha256:fc06b20b223c9afc76d3b0c1da4b541f616855de464c5f4d4592e3534c1aafc9", "bytes": 24305, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fendo.2020.00104", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7069359", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE46687", "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=GSE46687", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46687", "version": null, "note": "The datasets generated for this study can be found in the GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46687, using code GSE46687.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46687, using code GSE46687.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1134016", "GSM1134017", "GSM1134018", "GSM1134019", "GSM1134020", "GSM1134021", "GSM1134022", "GSM1134023", "GSM1134024", "GSM1134025", "GSM1134026", "GSM1134027", "GSM1134028", "GSM1134029", "GSM1134030", "GSM1134031", "GSM1134032", "GSM1134033", "GSM1134034", "GSM1134035", "GSM1134036", "GSM1134037", "GSM1134038", "GSM1134039", "GSM1134040", "GSM1134041", "GSM1134042", "GSM1134043", "GSM1134044", "GSM1134045", "GSM1134046", "GSM1134047", "GSM1134048", "GSM1134049", "GSM1134050", "GSM1134051"], "sample_count": 36, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Profiling in 45X Turner Syndrome patients", "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:32210915:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4b66b9b99a22d3a8cb14d84937d852a823ee636f2c6804b011eb49c41816c011", "bytes": 8962, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T1", "version": null, "note": "Differentially expressed genes of Turner Syndrome.", "structure": {"pmcid": "PMC7069359", "section_index": 9, "section_title": "Differentially Expressed Genes", "row_count": 89, "column_count": 7}, "table": {"label": "Table 1", "caption": "Differentially expressed genes of Turner Syndrome.", "rows": [["Gene symbol", "Adjusted P-value", "Fold change", "Gene title", "Location"], ["", "Xm-XX", "Xp-XX", "Xm-XX", "Xp-XX", "", ""], ["Up regulated genes"], ["ACVR2B", "1.79E-02", "8.62E-03", "4.659", "4.852", "Activin A receptor type 2B", "Chromosome 3"], ["AGER", "2.44E-02", "1.27E-02", "3.434", "3.729", "Advanced glycosylation end-product specific receptor", "Chromosome 6"], ["ANK1", "2.12E-02", "3.55E-03", "5.540", "2.630", "Ankyrin 1", "Chromosome 8"], ["B3GAT1", "4.31E-02", "3.80E-02", "4.993", "5.448", "Beta-1,3-glucuronyltransferase 1", "Chromosome 11"], ["BAZ2A", "1.73E-02", "1.35E-02", "2.639", "2.662", "Bromodomain adjacent to zinc finger domain 2A", "Chromosome 12"], ["BCL11B", "2.50E-02", "1.27E-02", "3.074", "3.550", "B-cell CLL/lymphoma 11B", "Chromosome 14"], ["C11orf53", "3.41E-02", "1.31E-02", "2.969", "2.701", "Chromosome 11 open reading frame 53", "Chromosome 11"], ["CEMP1", "3.83E-02", "4.53E-03", "2.114", "2.665", "Cementum protein 1", "Chromosome 16"], ["CYBA", "4.90E-02", "4.44E-03", "2.428", "2.951", "Cytochrome b-245 alpha chain", "Chromosome 16"], ["DGKK", "9.00E-04", "2.65E-02", "6.916", "4.562", "Diacylglycerol kinase kappa", "Chromosome X"], ["FAM229B", "4.53E-02", "2.20E-02", "2.969", "2.821", "Family with sequence similarity 229 member B", "Chromosome 6"], ["HDAC5", "2.13E-02", "2.05E-05", "2.173", "2.459", "Histone deacetylase 5", "Chromosome 17"], ["IGFBP2", "4.73E-02", "1.74E-02", "4.347", "3.908", "Insulin like growth factor binding protein 2", "Chromosome 2"], ["KDM6B", "7.00E-03", "8.66E-03", "3.387", "3.502", "Lysine demethylase 6B", "Chromosome 17"], ["KHSRP", "3.83E-02", "2.97E-02", "2.378", "2.391", "KH-type splicing regulatory protein", "Chromosome 19"], ["MED16", "4.89E-02", "1.17E-03", "2.042", "2.478", "Mediator complex subunit 16", "Chromosome 19"], ["MYL9", "2.95E-02", "3.45E-02", "10.411", "9.513", "Myosin light chain 9", "Chromosome 20"], ["OVCH1-AS1", "3.83E-02", "6.05E-03", "3.387", "4.555", "OVCH1 antisense RNA 1", "Chromosome 12"], ["PERM1", "3.12E-02", "3.24E-02", "2.713", "2.050", "PPARGC1 and ESRR induced regulator, muscle 1", "Chromosome 1"], ["PSMD5-AS1", "4.12E-02", "2.10E-02", "2.908", "2.748", "PSMD5 antisense RNA 1 (head to head)", "Chromosome 9"], ["SAFB2", "4.89E-02", "5.15E-03", "2.532", "3.022", "Scaffold attachment factor B2", "Chromosome 19"], ["SRCAP", "1.37E-02", "8.18E-05", "4.563", "6.930", "Snf2-related CREBBP activator protein", "Chromosome 16"], ["STK11", "6.00E-04", "2.48E-03", "6.063", "6.820", "Serine/threonine kinase 11", "Chromosome 19"], ["UBE2O", "9.00E-03", "4.44E-03", "2.549", "2.801", "Ubiquitin conjugating enzyme E2 O", "Chromosome 17"], ["ZMIZ2", "3.30E-02", "2.81E-02", "2.621", "2.793", "Zinc finger MIZ-type containing 2", "Chromosome 7"], ["Down regulated genes"], ["AFF3", "2.54E-02", "4.28E-02", "0.1934", "0.3026", "AF4/FMR2 family member 3", "Chromosome 2"], ["AGFG1", "3.41E-02", "3.37E-03", "0.4033", "0.4174", "ArfGAP with FG repeats 1", "Chromosome 2"], ["AHNAK", "6.80E-03", "2.74E-02", "0.2132", "0.2273", "AHNAK nucleoprotein", "Chromosome 11"], ["AP1S2*", "2.95E-02", "2.60E-03", "0.4263", "0.3898", "Adaptor related protein complex 1 sigma 2 subunit", "Chromosome X"], ["ASMTL", "3.60E-03", "3.50E-04", "0.4633", "0.4923", "Acetylserotonin O-methyltransferase-like", "Chromosome X"], ["ATRX", "1.68E-02", "1.32E-02", "0.3950", "0.4502", "ATRX, chromatin remodeler", "Chromosome X"], ["BID", "3.26E-02", "3.38E-03", "0.4796", "0.4956", "BH3 interacting domain death agonist", "Chromosome 22"], ["CARD16", "2.03E-02", "4.77E-03", "0.4569", "0.4879", "Caspase recruitment domain family member 16", "Chromosome 11"], ["CD99*", "2.01E-02", "3.58E-03", "0.4601", "0.4851", "CD99 molecule", "Chromosome X"], ["CDC27", "6.00E-04", "1.08E-04", "0.3711", "0.3945", "Cell division cycle 27", "Chromosome 17"], ["CHD9", "3.20E-03", "8.23E-03", "0.3078", "0.3351", "Chromodomain helicase DNA binding protein 9", "Chromosome 16"], ["CSF2RA*", "8.81E-03", "5.39E-04", "0.3099", "0.3510", "Colony stimulating factor 2 receptor alpha subunit", "Chromosome X"], ["CSGALNACT2", "5.94E-03", "1.18E-02", "0.3842", "0.3309", "Chondroitin sulfate N-acetylgalactosaminyltransferase 2", "Chromosome 10"], ["CXorf38", "4.00E-04", "3.40E-04", "0.3869", "0.3602", "Chromosome X open reading frame 38", "Chromosome X"], ["DHRSX", "2.50E-02", "6.05E-03", "0.2736", "0.2140", "Dehydrogenase/reductase X-linked", "Chromosome X"], ["DHX9", "3.08E-02", "2.78E-02", "0.4569", "0.4841", "DEAH-box helicase 9", "Chromosome 1"], ["EIF1AX", "3.41E-02", "5.57E-03", "0.4897", "0.4475", "Eukaryotic translation initiation factor 1A, X-linked", "Chromosome X"], ["EPRS", "1.79E-03", "5.92E-03", "0.4005", "0.3890", "Glutamyl-prolyl-tRNA synthetase", "Chromosome 1"], ["EREG", "8.39E-03", "4.73E-03", "0.2952", "0.3238", "Epiregulin", "Chromosome 4"], ["FCGR2C", "3.23E-03", "2.59E-02", "0.2365", "0.4009", "Fc fragment of IgG receptor Iic", "Chromosome 1"], ["FKBP15", "3.23E-03", "6.31E-03", "0.2813", "0.2773", "FK506 binding protein 15", "Chromosome 9"], ["FRG1JP", "4.90E-02", "1.61E-02", "0.3345", "0.3576", "FSHD region gene 1 family member J, pseudogene", "Chromosome 9"], ["FXR1", "3.23E-03", "2.98E-03", "0.3511", "0.3833", "FMR1 autosomal homolog 1", "Chromosome 3"], ["HADHA", "2.40E-03", "2.60E-03", "0.4263", "0.3944", "Hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), alpha subunit", "Chromosome 2"], ["HECTD1", "7.01E-03", "8.16E-03", "0.4730", "0.4768", "HECT domain E3 ubiquitin protein ligase 1", "Chromosome 14"], ["HES1", "4.11E-02", "3.19E-02", "0.2973", "0.4613", "Hes family bHLH transcription factor 1", "Chromosome 3"], ["IL1R2", "3.08E-02", "1.99E-02", "0.1627", "0.3489", "Interleukin 1 receptor type 2", "Chromosome 2"], ["INO80D", "2.00E-02", "5.42E-03", "0.2736", "0.2952", "INO80 complex subunit D", "Chromosome 2"], ["IQGAP1", "6.35E-04", "2.48E-03", "0.3487", "0.3747", "IQ motif containing GTPase activating protein 1", "Chromosome 15"], ["JAK1", "2.03E-02", "1.30E-02", "0.4538", "0.4758", "Janus kinase 1", "Chromosome 1"], ["KDM6A", "1.51E-02", "4.48E-03", "0.3896", "0.4880", "Lysine demethylase 6A", "Chromosome X"], ["KIAA1033", "1.50E-03", "2.77E-03", "0.3789", "0.4213", "KIAA1033", "Chromosome 12"], ["LOC100289090", "6.35E-04", "5.41E-03", "0.3392", "0.4276", "Uncharacterized LOC100289090", "Chromosome 15"], ["LOC101930114", "1.52E-02", "9.33E-03", "0.4005", "0.4218", "Uncharacterized LOC101930114", "Chromosome 1"], ["MAP4", "1.93E-02", "1.15E-02", "0.2774", "0.3805", "Microtubule associated protein 4", "Chromosome 3"], ["MYLPF", "3.41E-02", "3.58E-03", "0.2872", "0.1968", "Myosin light chain, phosphorylatable, fast skeletal muscle", "Chromosome 16"], ["NLRC4", "2.48E-02", "2.60E-02", "0.2793", "0.2312", "NLR family CARD domain containing 4", "Chromosome 2"], ["NSMAF", "8.98E-04", "5.51E-03", "0.3487", "0.2810", "Neutral sphingomyelinase activation associated factor", "Chromosome 8"], ["PLXNC1", "1.92E-02", "1.00E-02", "0.3487", "0.3616", "Plexin C1", "Chromosome 12"], ["PTPN12", "2.82E-02", "3.06E-02", "0.4147", "0.4630", "Protein tyrosine phosphatase, non-receptor type 12", "Chromosome 7"], ["RPL37A", "2.50E-02", "2.10E-02", "0.3209", "0.3612", "Ribosomal protein L37a", "Chromosome 2"], ["SAMHD1", "6.88E-03", "6.57E-03", "0.3842", "0.3232", "SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1", "Chromosome 20"], ["SLC25A6", "9.11E-04", "5.97E-06", "0.3711", "0.3762", "Solute carrier family 25 member 6", "Chromosome X"], ["SMC1A", "8.81E-03", "2.03E-03", "0.1661", "0.3258", "Structural maintenance of chromosomes 1A", "Chromosome X"], ["SON", "9.93E-03", "6.67E-03", "0.4175", "0.4495", "SON DNA binding protein", "Chromosome 21"], ["SSFA2", "1.68E-02", "9.56E-03", "0.3164", "0.3670", "Sperm specific antigen 2", "Chromosome 2"], ["TAOK1", "2.66E-02", "3.55E-03", "0.4965", "0.4375", "TAO kinase 1", "Chromosome 17"], ["TIA1", "2.30E-02", "8.62E-03", "0.3978", "0.4613", "TIA1 cytotoxic granule-associated RNA binding protein", "Chromosome 2"], ["TOB1", "3.41E-02", "3.21E-02", "0.3711", "0.4056", "Transducer of ERBB2, 1", "Chromosome 17"], ["TOP1", "3.83E-02", "4.06E-03", "0.4538", "0.4516", "Topoisomerase (DNA) I", "Chromosome 20"], ["TPP2", "4.59E-02", "2.60E-03", "0.4601", "0.4281", "Tripeptidyl peptidase 2", "Chromosome 13"], ["TSIX", "2.52E-06", "8.18E-05", "0.0769", "0.0495", "TSIX transcript, XIST antisense RNA", "Chromosome X"], ["USP10", "8.02E-03", "2.97E-03", "0.3842", "0.4655", "Ubiquitin specific peptidase 10", "Chromosome 16"], ["VPS13B", "1.94E-02", "3.46E-02", "0.3816", "0.3808", "Vacuolar protein sorting 13 homolog B", "Chromosome 8"], ["VPS35", "2.50E-02", "8.24E-03", "0.3392", "0.3926", "VPS35 retromer complex component", "Chromosome 16"], ["XIST", "3.48E-14", "2.64E-08", "0.0042", "0.0019", "X inactive specific transcript (non-protein coding)", "Chromosome X"], ["ZBTB38", "2.43E-03", "1.34E-02", "0.4538", "0.4446", "Zinc finger and BTB domain containing 38", "Chromosome 3"], ["ZFX", "2.95E-02", "5.70E-03", "0.4353", "0.4679", "Zinc finger protein, X-linked", "Chromosome X"], ["ZG16B", "1.30E-03", "6.51E-03", "0.2031", "0.2638", "Zymogen granule protein 16B", "Chromosome 16"], ["ZNF652", "3.41E-02", "1.99E-02", "0.3439", "0.3698", "Zinc finger protein 652", "Chromosome 17"]], "row_count": 89, "column_count": 7, "numeric_cells": 495, "header_rows": 2, "locator": "section[9]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32210915:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e1eea4e106f88603343bf22da3b3887690e12944b0ef0cd43fd0afe7012e540e", "bytes": 488, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T2", "version": null, "note": "Tissue-specific expressed genes identified by BioGPS.", "structure": {"pmcid": "PMC7069359", "section_index": 10, "section_title": "Tissue-Specific Expression of Genes", "row_count": 7, "column_count": 2}, "table": {"label": "Table 2", "caption": "Tissue-specific expressed genes identified by BioGPS.", "rows": [["System", "Genes"], ["Hematologic/immune", "ANK1, AGFG1, BID, CD99, CDC27, DHX9, EIF1AX, EPRS, EREG, FXR1, IL1R2, IQGAP1, KIAA1033, PLXNC1, SON, TOP1"], ["Neurologic", "B3GAT1, XIST"], ["Skin/skeletal muscle", "HES1, MYLPF"], ["Respiratory", "AGER"], ["Digestive", "IGFBP2"], ["Circulatory", "MYL9"]], "row_count": 7, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:32210915:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b426d54c8e16b06bd3ceb5de6238604c5eb3b32787c59dd1fffcc3309febf1b6", "bytes": 3071, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T3", "version": null, "note": "The enriched terms for DEGs.", "structure": {"pmcid": "PMC7069359", "section_index": 11, "section_title": "Functional and Pathway Enrichment of DEGs", "row_count": 12, "column_count": 6}, "table": {"label": "Table 3", "caption": "The enriched terms for DEGs.", "rows": [["Category", "Term", "Description", "Count", "Genes", "P-value"], ["UP_KEYWORDS", "/", "Phosphoprotein", "57", "KDM6A, CXORF38, IQGAP1, ZBTB38, TOP1, NLRC4, ANK1, TPP2, ASMTL, KIAA1033, USP10, VPS13B, INO80D, AHNAK, ZFX, UBE2O, ACVR2B, KHSRP, FKBP15, SRCAP, KDM6B, BID, PLXNC1, AGFG1, STK11, SSFA2, HADHA, ZNF652, MYL9, CHD9, BCL11B, VPS35, BAZ2A, HECTD1, DHX9, TAOK1, EPRS, CD99, SAMHD1, DGKK, AFF3, MYLPF, AGER, CDC27, PTPN12, FXR1, SAFB2, HDAC5, ATRX, CYBA, B3GAT1, SON, FCGR2C, JAK1, MAP4, SMC1A, TOB1", "6.04E-09"], ["GOTERM_MF_DIRECT", "GO:0005515", "Protein binding", "57", "IQGAP1, ZBTB38, TOP1, NLRC4, AP1S2, ANK1, TPP2, ASMTL, TIA1, EIF1AX, USP10, NSMAF, AHNAK, CSF2RA, SLC25A6, HES1, UBE2O, ACVR2B, EREG, MED16, ZMIZ2, KHSRP, FKBP15, SRCAP, KDM6B, BID, IL1R2, PLXNC1, AGFG1, STK11, HADHA, ZNF652, BCL11B, VPS35, BAZ2A, HECTD1, DHX9, TAOK1, EPRS, SAMHD1, AGER, CDC27, PTPN12, FXR1, SAFB2, HDAC5, ATRX, CYBA, SON, FCGR2C, CSGALNACT2, JAK1, MAP4, RPL37A, SMC1A, IGFBP2, TOB1", "1.72E-07"], ["UP_KEYWORDS", "/", "Methylation", "15", "DHX9, KDM6A, CXORF38, STK11, SLC25A6, MYLPF, EPRS, HADHA, SAFB2, ATRX, SON, ZMIZ2, BCL11B, KHSRP, AHNAK", "1.81E-05"], ["UP_KEYWORDS", "/", "Acetylation", "29", "BID, STK11, HADHA, IQGAP1, MYL9, CHD9, TOP1, TPP2, BCL11B, TIA1, KIAA1033, USP10, BAZ2A, AHNAK, DHX9, SLC25A6, SAMHD1, EPRS, PTPN12, SAFB2, FXR1, ATRX, HDAC5, SON, KHSRP, FKBP15, MAP4, JAK1, SMC1A", "2.33E-05"], ["UP_KEYWORDS", "/", "Ubl conjugation", "19", "BID, SSFA2, SAMHD1, SAFB2, ZBTB38, HDAC5, ATRX, CHD9, TOP1, UBE2O, SON, ZMIZ2, BCL11B, EIF1AX, KHSRP, MAP4, USP10, BAZ2A, AHNAK", "4.44E-05"], ["GOTERM_CC_DIRECT", "GO:0005634", "Nucleus", "38", "KDM6A, STK11, SSFA2, ZNF652, IQGAP1, ZBTB38, CHD9, TOP1, NLRC4, ANK1, TPP2, BCL11B, USP10, INO80D, BAZ2A, AHNAK, HECTD1, DHX9, SLC25A6, ZFX, AFF3, SAMHD1, CDC27, SAFB2, ATRX, HES1, HDAC5, UBE2O, CYBA, ZMIZ2, MED16, PERM1, JAK1, RPL37A, SMC1A, SRCAP, KDM6B, TOB1", "6.28E-05"], ["UP_KEYWORDS", "/", "Isopeptide bond", "15", "SSFA2, ZBTB38, SAFB2, ATRX, TOP1, CHD9, SON, ZMIZ2, TPP2, BCL11B, EIF1AX, KHSRP, MAP4, BAZ2A, AHNAK", "6.95E-05"], ["GOTERM_CC_DIRECT", "GO:0005737", "Cytoplasm", "36", "BID, IL1R2, STK11, SSFA2, IQGAP1, CHD9, ANK1, TPP2, ASMTL, TIA1, USP10, NSMAF, BAZ2A, AHNAK, HECTD1, DHX9, TAOK1, DGKK, CD99, AFF3, EPRS, CDC27, PTPN12, FXR1, SAFB2, HES1, HDAC5, UBE2O, ACVR2B, FCGR2C, PERM1, CEMP1, JAK1, MAP4, SMC1A, TOB1", "1.86E-04"], ["GOTERM_MF_DIRECT", "GO:0044822", "Poly(A) RNA binding", "14", "DHX9, FXR1, SAFB2, TOP1, UBE2O, SON, EIF1AX, TIA1, KHSRP, MAP4, RPL37A, USP10, SMC1A, AHNAK", "4.98E-04"], ["UP_KEYWORDS", "/", "Chromatin regulator", "7", "ATRX, HDAC5, CHD9, KDM6A, SRCAP, BAZ2A, KDM6B", "7.22E-04"], ["UP_KEYWORDS", "/", "Nucleus", "33", "KDM6A, AGFG1, STK11, ZNF652, ZBTB38, CHD9, TOP1, TPP2, BCL11B, TIA1, USP10, BAZ2A, INO80D, AHNAK, DHX9, ZFX, SAMHD1, AFF3, CDC27, SAFB2, ATRX, HES1, HDAC5, UBE2O, SON, ZMIZ2, MED16, PERM1, KHSRP, SMC1A, SRCAP, KDM6B, TOB1", "1.46E-03"]], "row_count": 12, "column_count": 6, "numeric_cells": 36, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:32210915:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdb444fd2a887c71d9568a77deeddc56ab376b62c3b4a3ec70f3b8ef6073b97e", "bytes": 866, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T4", "version": null, "note": "Genes of interest.", "structure": {"pmcid": "PMC7069359", "section_index": 13, "section_title": "Identification of Genes of Interest", "row_count": 18, "column_count": 6}, "table": {"label": "Table 4", "caption": "Genes of interest.", "rows": [["Up-regulated", "", "Down-regulated", ""], ["Gene", "Fold change", "Gene", "Fold change"], ["", "Xm-XX", "Xp-XX", "", "Xm-XX", "Xp-XX"], ["HEMATOLOGIC/IMMUNE SYSTEM"], ["UBE2O", "2.549", "2.801", "CDC27", "0.3711", "0.3945"], ["AGER", "3.434", "3.729", "CD99", "0.4601", "0.4851"], ["ANK1", "5.540", "2.630", "HECTD1", "0.4730", "0.4768"], ["", "", "", "CSF2RA", "0.3099", "0.3510"], ["", "", "", "AP1S2", "0.4263", "0.3898"], ["", "", "", "DHX9", "0.4569", "0.4841"], ["", "", "", "EREG", "0.2952", "0.3238"], ["", "", "", "IL1R2", "0.1627", "0.3489"], ["", "", "", "PLXNC1", "0.3487", "0.3616"], ["CIRCULATORY SYSTEM"], ["MYL9", "10.411", "9.513", "MYLPF", "0.2872", "0.1968"], ["METABOLISM SYSTEM"], ["IGFBP2", "4.347", "3.908", "", "", ""], ["B3GAT1", "4.993", "5.448", "", "", ""]], "row_count": 18, "column_count": 6, "numeric_cells": 34, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T4"}}], "gaps": ["asset:data:geo:GSE46687 not downloaded", "asset:data:geo:GSE46687 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": null, "specific": null, "label": "t-tests using GEO2R; source data obtained from GEO dataset GSE46687", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential expression analysis was performed using the online analysis tool GEO2R; the expression profiles of monosomy X TS patients and normal 46,XX females were compared to identify the DEGs. P-values and adjusted P-values were calculated using t-tests."}}], "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": ["GSE46687"], "resolved_accessions": ["GSE46687"], "statements": ["The datasets generated for this study can be found in the GEO dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46687, using code GSE46687."], "basis": "The paper names GSE46687 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:32210915", "data:geo:GSE46687", "asset:table:pmid:32210915:1", "asset:table:pmid:32210915:2", "asset:table:pmid:32210915:3", "asset:table:pmid:32210915:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE46687"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:18:51Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18024, "completion_tokens": 1304, "cached_tokens": 792}}, "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:32210915", "type": "paper", "label": "pmid:32210915"}, {"id": "source:pmid:32210915", "type": "manuscript", "label": "PMID 32210915 full text"}, {"id": "data:geo:GSE46687", "type": "dataset", "label": "GEO GSE46687"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32210915", "type": "paper", "label": "pmid:32210915"}, {"id": "source:pmid:32210915", "type": "manuscript", "label": "PMID 32210915 full text"}, {"id": "data:geo:GSE46687", "type": "dataset", "label": "GEO GSE46687"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32210915", "type": "extraction", "used": ["source:pmid:32210915"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE46687", "type": "accession_resolution", "used": ["data:geo:GSE46687"], "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:32210915", "parent_hash": "sha256:b45d33da4e33e1af165c6ed749f5733d1f94cd257501db6d71aae51ba6aa2855", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE46687 licence not read", "asset:data:geo:GSE46687 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["sed the online Gene Expression Omnibus (GEO) microarray expression profiling dataset GSE46687 to ide"], "order_basis": "paper_text_order:382", "id": "assay:1"}, {"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": "consumes_earlier_output", "id": "assay:2"}]}