Identification of GINS1 as a potential prognostic biomarker for sarcoma using bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37180662", "kind": "science-record", "revision": 4, "content_hash": "sha256:5faae940ffc311189e1e9e9427e151f367464d154dbe00dcd29450502fa460a2", "created_at": "2026-11-01T19:01:51Z", "updated_at": "2026-11-01T22:51:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of GINS1 as a potential prognostic biomarker for sarcoma using bioinformatic analysis.", "doi": "10.21037/tcr-23-524", "pmid": "37180662", "authors": ["Huanhuan Zhao", "Xiaoxia He", "Zhanbei Ma"], "journal": "Translational cancer research", "year": 2023, "abstract": "Background: The GINS complex is related to cancer development, invasion, and poor prognosis in multiple tumors. In the study, we attempted to investigate the prognostic value of GINS1 in sarcoma patients.\nMethods: We analyzed GINS1 expression using Tumor IMmune Estimation Resource (TIMER) 2.0, Gene Expression Omnibus (GEO; GSE21122, GSE39262, and GSE21050), and The Cancer Genome Atlas (TCGA) databases. The prognostic value of GINS1 was explored using the survival and survminer packages of R. Genetic alteration analysis was investigated using cBioPortal. The Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) R script was used for the immunocyte infiltration analysis. MicroRNAs (miRNAs) targeting GINS1 were predicted using GEO (GSE69470) and MicroRNA Target Prediction Database (miRDB).\nResults: We found that GINS1 was overexpressed in sarcoma, especially in metastatic samples, and was associated with a worse prognosis. High GINS1 expression was a poor prognostic indicator for sarcoma patients. Moreover, GINS1 alteration was associated with worse survival of sarcoma patients. Immune infiltration analysis indicated that GINS1 expression was correlated with the infiltration of M0 and M2 macrophages in sarcoma. Finally, the miRNA hsa-miR-376a-3p was identified to potentially regulate GINS1 in sarcoma.\nConclusions: These results indicate that GINS1 may be a promising prognostic biomarker and therapeutic target for sarcoma.", "claims": [{"id": "claim-method", "statement": "Overall survival (OS) and multivariate Cox regression analyses of sarcoma patients were performed by the survival and survminer packages in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180662", "locator": "sections[6] \"Survival analysis\" paragraph 2", "quote": "Overall survival (OS) and multivariate Cox regression analyses of sarcoma patients were performed by the survival and survminer packages in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "A total of 174 sarcoma patients with complete metastasis information were obtained from The Cancer Genome Atlas (TCGA; https://cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) (20) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37180662", "locator": "sections[5] \"Expression level analysis of GINS1 in metastatic sarcoma\" paragraph 2", "quote": "A total of 174 sarcoma patients with complete metastasis information were obtained from The Cancer Genome Atlas (TCGA; https://cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) (20) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Compared with low GINS1 expression, sarcoma patients with high GINS1 expression had a higher risk of death [hazard ratio (HR) = 1.80, 95% confidence interval (CI): 1.185–2.7, P=0.006, Figure 3B], indicating that high GINS1 expression was a poor prognostic indicator for sarcomas.", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Compared with low GINS1 expression, sarcoma patients with high GINS1 expression had a higher risk of death [hazard ratio (HR) = 1.80, 95% confidence interval (CI): 1.185–2.7, P=0.006, Figure 3B], indicating that high GINS1 expression was a poor prognostic indicator for sarcomas."}, "evidence": [{"asset": "source:pmid:37180662", "locator": "sections[14] \"The prognostic value of GINS1 in sarcoma\" paragraph 4", "quote": "Compared with low GINS1 expression, sarcoma patients with high GINS1 expression had a higher risk of death [hazard ratio (HR) = 1.80, 95% confidence interval (CI): 1.185–2.7, P=0.006, Figure 3B], indicating that high GINS1 expression was a poor prognostic indicator for sarcomas."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Compared with low GINS1 expression, sarcoma patients with high GINS1 expression had a higher risk of death [hazard ratio (HR) = 1.80, 95% confidence interval (CI): 1.185–2.7, P=0.006, Figure 3B], indicating that high GINS1 expression was a poor prognostic indicator for sarcomas.", "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:37180662"], "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:GSE21050"], "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:GSE21050"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37180662", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-23-524", "sha256": 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No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "cox_ph", "expected_value": 0.006, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE21122", "GSE39262", "GSE21050", "GSE69470"], "resolved_accessions": ["GSE21122", "GSE39262", "GSE21050", "GSE69470"], "statements": ["A total of 174 sarcoma patients with complete metastasis information were obtained from The Cancer Genome Atlas (TCGA; https://cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) (20) database."], "basis": "The paper names GSE21122, GSE39262, GSE21050, GSE69470 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:37180662", "data:geo:GSE21050"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21050"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:39:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9205, "completion_tokens": 2067, "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:37180662", "type": "paper", "label": "pmid:37180662"}, {"id": "source:pmid:37180662", "type": "manuscript", "label": "PMID 37180662 full text"}, {"id": "data:geo:GSE21050", "type": "dataset", "label": "GEO GSE21050"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37180662", "type": "paper", "label": "pmid:37180662"}, {"id": "source:pmid:37180662", "type": "manuscript", "label": "PMID 37180662 full text"}, {"id": "data:geo:GSE21050", "type": "dataset", "label": "GEO GSE21050"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37180662", "type": "extraction", "used": ["source:pmid:37180662"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21050", "type": "accession_resolution", "used": ["data:geo:GSE21050"], "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:37180662", "parent_hash": "sha256:e628f0eed7c1f55667d134752fd20138450fa2ade8ccda2e128cf187807d4da8", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE21050 licence not read", "asset:data:geo:GSE21050 not downloaded", "asset:data:geo:GSE21122 licence not read", "asset:data:geo:GSE21122 not downloaded", "asset:data:geo:GSE39262 licence not read", "asset:data:geo:GSE39262 not downloaded", "asset:data:geo:GSE69470 licence not read", "asset:data:geo:GSE69470 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "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": 0.99, "evidence": ["untransformed primary cells were detected by Affymetrix Human Genome U133A Array (Affymetrix, Santa", "cted by Affymetrix Human Genome U133A Array (Affymetrix, Santa Clara, CA, USA). Differential express"], "order_basis": "paper_text_order:2159", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Overall survival (OS) and multivariate Cox regression analyses of sarcoma patients were performed by the survival and survminer packages in R."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}