Bioinformatics Analysis of ZBTB16 as a Prognostic Marker for Ewing's Sarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34660783", "kind": "science-record", "revision": 5, "content_hash": "sha256:2c650e26c67a0d6423ebe6ae2a917e7ec00fd9e483897108cf93093aee3b7456", "created_at": "2026-11-01T17:36:19Z", "updated_at": "2026-11-01T22:47:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of ZBTB16 as a Prognostic Marker for Ewing's Sarcoma.", "doi": "10.1155/2021/1989917", "pmid": "34660783", "authors": ["Ke Ding", "Wenli Qiu", "Dianbo Yu", "Huade Ma", "Kangqi Xie", "Fuqiang Luo", "Shanlang Li", "Zaiyong Li", "Jihua Wei"], "journal": "BioMed research international", "year": 2021, "abstract": "OBJECTIVE: The purpose of this study is to identify novel biomarkers for the prognosis of Ewing's sarcoma based on bioinformatics analysis.\nMETHODS: The GSE63157 and GSE17679 datasets contain patient and healthy control microarray data that were downloaded from the Gene Expression Omnibus (GEO) database and analyzed through R language software to obtain differentially expressed genes (DEGs). Firstly, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment, protein-protein interaction (PPI) networks, and Cytoscape Molecular Complex Detection (MCODE) plug-in were then used to compute the highest scores of the module. After survival analysis, the hub genes were lastly obtained from the two module genes.\nRESULTS: A total of 1181 DEGs were identified from the two GSEs. Through MCODE and survival analysis, we obtain 53 DEGs from the module and 29 overall survival- (OS-) related genes. ZBTB16 was the only downregulated gene after Venn diagrams. Survival analysis indicates that there was a significant correlation between the high expression of ZBTB16 and the OS of Ewing's sarcoma (ES), and the low expression group had an unfavorable OS when compared to the high expression group.\nCONCLUSIONS: High expression of ZBTB16 may serve as a predictor biomarker of poor prognosis in ES patients.", "claims": [{"id": "claim-method", "statement": "Univariate and multivariate Cox regression analyses showed that ZBTB16 may be a prognostic factor for ES. The difference is statistically significant (P < 0.01) (Figure 5).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34660783", "locator": "sections[14] \"3.6. Survival Analysis of Hub Gene\" paragraph 2", "quote": "Univariate and multivariate Cox regression analyses showed that ZBTB16 may be a prognostic factor for ES. The difference is statistically significant (P < 0.01) (Figure 5)."}], "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:34660783", "locator": "sections[18] \"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"}, {"id": "claim-target-result", "statement": "A total of 1181 DEGs were identified from GSE63157 and GSE17679 datasets, of which 364 were upregulated genes and 817 were downregulated genes (Figure 2(a)).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34660783", "locator": "sections[10] \"3.2. Identification of DEGs\" paragraph 2", "quote": "A total of 1181 DEGs were identified from GSE63157 and GSE17679 datasets, of which 364 were upregulated genes and 817 were downregulated genes (Figure 2(a))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1181 DEGs were identified from GSE63157 and GSE17679 datasets, of which 364 were upregulated genes and 817 were downregulated genes (Figure 2(a)).", "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:34660783"], "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:GSE17679"], "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:GSE17679"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34660783", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/1989917", "sha256": "sha256:485901ad577f88dab0481b5efb8251ab8034a2a8844217592d07cc64a9cd7787", "bytes": 14740, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/1989917", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8514890", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17679", "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=GSE17679", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17679", "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": ["GSM439886", "GSM439887", "GSM439888", "GSM439889", "GSM439890", "GSM439891", "GSM439892", "GSM439893", "GSM439894", "GSM439895", "GSM439896", "GSM439897", "GSM439898", "GSM439899", "GSM439900", "GSM439901", "GSM439902", "GSM439903", "GSM439904", "GSM439905", "GSM439906", "GSM439907", "GSM439908", "GSM439909", "GSM439910", "GSM439911", "GSM439912", "GSM439913", "GSM439914", "GSM439915", "GSM439916", "GSM439917", "GSM439918", "GSM439919", "GSM439920", "GSM439921", "GSM439922", "GSM439923", "GSM439924", "GSM439925", "GSM439926", "GSM439927", "GSM439928", "GSM439929", "GSM439930", "GSM439931", "GSM439932", "GSM439933", "GSM439934", "GSM439935", "GSM439936", "GSM439937", "GSM439938", "GSM439939", "GSM439940", "GSM440999", "GSM441000", "GSM441001", "GSM441002", "GSM441003", "GSM441004", "GSM441005", "GSM441006", "GSM441007", "GSM441008", "GSM441009", "GSM441010", "GSM441011", "GSM441012", "GSM441013", "GSM441014", "GSM441015", "GSM441016", "GSM441017", "GSM441018", "GSM441019", "GSM441020", "GSM441021", "GSM441022", "GSM441023", "GSM441024", "GSM441025", "GSM441026", "GSM441027", "GSM441028", "GSM441029", "GSM441030", "GSM441031", "GSM441032", "GSM441033", "GSM441034", "GSM441035", "GSM441036", "GSM441037", "GSM441038", "GSM441039", "GSM441040", "GSM441041", "GSM441042", "GSM441044", "GSM441045", "GSM441046", "GSM441047", "GSM441048", "GSM441049", "GSM441050", "GSM441051", "GSM441052", "GSM441053", "GSM441054", "GSM441055", "GSM441056", "GSM441057", "GSM441058", "GSM441059", "GSM441060", "GSM441061"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Inflammatory gene profiling of Ewing sarcoma family of tumors", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE63157", "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=GSE63157", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63157", "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": ["GSM1542334", "GSM1542335", "GSM1542336", "GSM1542337", "GSM1542338", "GSM1542339", "GSM1542340", "GSM1542341", "GSM1542342", "GSM1542343", "GSM1542344", "GSM1542345", "GSM1542346", "GSM1542347", "GSM1542348", "GSM1542349", "GSM1542350", "GSM1542351", "GSM1542352", "GSM1542353", "GSM1542354", "GSM1542355", "GSM1542356", "GSM1542357", "GSM1542358", "GSM1542359", "GSM1542360", "GSM1542361", "GSM1542362", "GSM1542363", "GSM1542364", "GSM1542365", "GSM1542366", "GSM1542367", "GSM1542368", "GSM1542369", "GSM1542370", "GSM1542371", "GSM1542372", "GSM1542373", "GSM1542374", "GSM1542375", "GSM1542376", "GSM1542377", "GSM1542378", "GSM1542379", "GSM1542380", "GSM1542381", "GSM1542382", "GSM1542383", "GSM1542384", "GSM1542385", "GSM1542386", "GSM1542387", "GSM1542388", "GSM1542389", "GSM1542390", "GSM1542391", "GSM1542392", "GSM1542393", "GSM1542394", "GSM1542395", "GSM1542396", "GSM1542397", "GSM1542398", "GSM1542399", "GSM1542400", "GSM1542401", "GSM1542402", "GSM1542403", "GSM1542404", "GSM1542405", "GSM1542406", "GSM1542407", "GSM1542408", "GSM1542409", "GSM1542410", "GSM1542411", "GSM1542412", "GSM1542413", "GSM1542414", "GSM1542415", "GSM1542416", "GSM1542417", "GSM1542418"], "sample_count": 85, "group_sizes": null, "group_sizes_basis": null, "platform": "5175", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions: A Report from the Children's Oncology Group", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE17679 not downloaded", "asset:data:geo:GSE17679 licence not read", "asset:data:geo:GSE63157 not downloaded", "asset:data:geo:GSE63157 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Univariate and multivariate Cox regression analyses showed that ZBTB16 may be a prognostic factor for ES. The difference is statistically significant (P < 0.01) (Figure 5)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE63157", "GSE17679"], "resolved_accessions": ["GSE63157", "GSE17679"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE63157, GSE17679 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": ["survival_km"], "assets": ["source:pmid:34660783", "data:geo:GSE17679"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17679"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:04:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 5575, "completion_tokens": 1564, "cached_tokens": 128}}, "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:34660783", "type": "paper", "label": "pmid:34660783"}, {"id": "source:pmid:34660783", "type": "manuscript", "label": "PMID 34660783 full text"}, {"id": "data:geo:GSE17679", "type": "dataset", "label": "GEO GSE17679"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34660783", "type": "paper", "label": "pmid:34660783"}, {"id": "source:pmid:34660783", "type": "manuscript", "label": "PMID 34660783 full text"}, {"id": "data:geo:GSE17679", "type": "dataset", "label": "GEO GSE17679"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34660783", "type": "extraction", "used": ["source:pmid:34660783"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17679", "type": "accession_resolution", "used": ["data:geo:GSE17679"], "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:34660783", "parent_hash": "sha256:5c87bd9f18915ce46a25931cdff2062537058e7a96edac39dc7d83cfe4080613", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE17679 licence not read", "asset:data:geo:GSE17679 not downloaded", "asset:data:geo:GSE63157 licence not read", "asset:data:geo:GSE63157 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate and multivariate Cox regression analyses showed that ZBTB16 may be a prognostic factor for ES. The difference is statistically significant (P < 0.01) (Figure 5)."], "order_basis": "analysis_only", "id": "assay:1"}]}