← All .science files
pmid:34066132
Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker.
Ssu-Han Chen · Hong-Han Lin · Yao-Feng Li · Wen-Chiuan Tsai · Dueng-Yuan Hueng
Cancers · 2021 doi:10.3390/cancers13102338
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 5 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 284 items
gaps array · 2 items
analysis object · 4 fields
methods array · 4 items
[0] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 4 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 4 items
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 5 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[4] object · 11 fields
required_operations array · 4 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34066132", "kind": "science-record", "revision": 7, "content_hash": "sha256:88e80f376ee591ed6040dc1041c2cb26fbb6e2b58c20c8c9159ab9f6c17e8127", "created_at": "2026-11-01T15:41:37Z", "updated_at": "2026-11-01T22:03:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Clinical Significance and Systematic Expression Analysis of the Thyroid Receptor Interacting Protein 13 (TRIP13) as Human Gliomas Biomarker.", "doi": "10.3390/cancers13102338", "pmid": "34066132", "authors": ["Ssu-Han Chen", "Hong-Han Lin", "Yao-Feng Li", "Wen-Chiuan Tsai", "Dueng-Yuan Hueng"], "journal": "Cancers", "year": 2021, "abstract": "The prognosis of malignant gliomas such as glioblastoma multiforme (GBM) has remained poor due to limited therapeutic strategies. Thus, it is pivotal to determine prognostic factors for gliomas. Thyroid Receptor Interacting Protein 13 (TRIP13) was found to be overexpressed in several solid tumors, but its role and clinical significance in gliomas is still unclear. Here, we conducted a comprehensive expression analysis of TRIP13 to determine the prognostic values. Gene expression profiles of the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA) and GSE16011 dataset showed increased TRIP13 expression in advanced stage and worse prognosis in IDH-wild type lower-grade glioma. We performed RT-PCR and Western blot to validate TRIP13 mRNA expression and protein levels in GBM cell lines. TRIP13 co-expressed genes via database screening were regulated by essential cancer-related upstream regulators (such as TP53 and FOXM1). Then, TCGA analysis revealed that more TRIP13 promoter hypomethylation was observed in GBM than in low-grade glioma. We also inferred that the upregulated TRIP13 levels in gliomas could be regulated by dysfunction of miR-29 in gliomas patient cohorts. Moreover, TRIP13-expressing tumors not only had higher aneuploidy but also tended to reduce the ratio of CD8+/Treg, which led to a worse survival outcome. Overall, these findings demonstrate that TRIP13 has with multiple functions in gliomas, and they may be crucial for therapeutic potential.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier survival analysis was performed to estimate the effect of TRIP13 expression on overall survival (OS) and progression-free survival (PFS) from TCGA, CGGA and GSE data.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34066132", "locator": "sections[14] \"4.1. Datasets, Glioma Samples and Survival Analysis\" paragraph 2", "quote": "The Kaplan–Meier survival analysis was performed to estimate the effect of TRIP13 expression on overall survival (OS) and progression-free survival (PFS) from TCGA, CGGA and GSE data."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All source data relating to this manuscript are available upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34066132", "locator": "sections[31] \"notes\" paragraph 1", "quote": "All source data relating to this manuscript are available upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34066132"], "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:GSE16011"], "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:GSE16011"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34066132", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/cancers13102338", "sha256": "sha256:878efbfbabfb1588f40c960cacab327108c013fbdfaf50571f4c83b236124532", "bytes": 63468, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/cancers13102338", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8150328", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16011", "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=GSE16011", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16011", "version": null, "note": "All source data relating to this manuscript are available upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All source data relating to this manuscript are available upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM405200", "GSM405201", "GSM405202", "GSM405203", "GSM405204", "GSM405205", "GSM405206", "GSM405207", "GSM405208", "GSM405209", "GSM405210", "GSM405211", "GSM405212", "GSM405213", "GSM405214", "GSM405215", "GSM405216", "GSM405217", "GSM405218", "GSM405219", "GSM405220", "GSM405221", "GSM405222", "GSM405223", "GSM405224", "GSM405225", "GSM405226", "GSM405227", "GSM405228", "GSM405229", "GSM405230", "GSM405231", "GSM405232", "GSM405233", "GSM405234", "GSM405235", "GSM405236", "GSM405237", "GSM405238", "GSM405239", "GSM405240", "GSM405241", "GSM405242", "GSM405243", "GSM405244", "GSM405245", "GSM405246", "GSM405247", "GSM405248", "GSM405249", "GSM405250", "GSM405251", "GSM405252", "GSM405253", "GSM405254", "GSM405255", "GSM405256", "GSM405257", "GSM405258", "GSM405259", "GSM405260", "GSM405261", "GSM405262", "GSM405263", "GSM405264", "GSM405265", "GSM405266", "GSM405267", "GSM405268", "GSM405269", "GSM405270", "GSM405271", "GSM405272", "GSM405273", "GSM405274", "GSM405275", "GSM405276", "GSM405277", "GSM405278", "GSM405279", "GSM405280", "GSM405281", "GSM405282", "GSM405283", "GSM405284", "GSM405285", "GSM405286", "GSM405287", "GSM405288", "GSM405289", "GSM405290", "GSM405291", "GSM405292", "GSM405293", "GSM405294", "GSM405295", "GSM405296", "GSM405297", "GSM405298", "GSM405299", "GSM405300", "GSM405301", "GSM405302", "GSM405303", "GSM405304", "GSM405305", "GSM405306", "GSM405307", "GSM405308", "GSM405309", "GSM405310", "GSM405311", "GSM405312", "GSM405313", "GSM405314", "GSM405315", "GSM405316", "GSM405317", "GSM405318", "GSM405319", "GSM405320", "GSM405321", "GSM405322", "GSM405323", "GSM405324", "GSM405325", "GSM405326", "GSM405327", "GSM405328", "GSM405329", "GSM405330", "GSM405331", "GSM405332", "GSM405333", "GSM405334", "GSM405335", "GSM405336", "GSM405337", "GSM405338", "GSM405339", "GSM405340", "GSM405341", "GSM405342", "GSM405343", "GSM405344", "GSM405345", "GSM405346", "GSM405347", "GSM405348", "GSM405349", "GSM405350", "GSM405351", "GSM405352", "GSM405353", "GSM405354", "GSM405355", "GSM405356", "GSM405357", "GSM405358", "GSM405359", "GSM405360", "GSM405361", "GSM405362", "GSM405363", "GSM405364", "GSM405365", "GSM405366", "GSM405367", "GSM405368", "GSM405369", "GSM405370", "GSM405371", "GSM405372", "GSM405373", "GSM405374", "GSM405375", "GSM405376", "GSM405377", "GSM405378", "GSM405379", "GSM405380", "GSM405381", "GSM405382", "GSM405383", "GSM405384", "GSM405385", "GSM405386", "GSM405387", "GSM405388", "GSM405389", "GSM405390", "GSM405391", "GSM405392", "GSM405393", "GSM405394", "GSM405395", "GSM405396", "GSM405397", "GSM405398", "GSM405399", "GSM405400", "GSM405401", "GSM405402", "GSM405403", "GSM405404", "GSM405405", "GSM405406", "GSM405407", "GSM405408", "GSM405409", "GSM405410", "GSM405411", "GSM405412", "GSM405413", "GSM405414", "GSM405415", "GSM405416", "GSM405417", "GSM405418", "GSM405419", "GSM405420", "GSM405421", "GSM405422", "GSM405423", "GSM405424", "GSM405425", "GSM405426", "GSM405427", "GSM405428", "GSM405429", "GSM405430", "GSM405431", "GSM405432", "GSM405433", "GSM405434", "GSM405435", "GSM405436", "GSM405437", "GSM405438", "GSM405439", "GSM405440", "GSM405441", "GSM405442", "GSM405443", "GSM405444", "GSM405445", "GSM405446", "GSM405447", "GSM405448", "GSM405449", "GSM405450", "GSM405451", "GSM405452", "GSM405453", "GSM405454", "GSM405455", "GSM405456", "GSM405457", "GSM405458", "GSM405459", "GSM405460", "GSM405461", "GSM405462", "GSM405463", "GSM405464", "GSM405465", "GSM405466", "GSM405467", "GSM405468", "GSM405469", "GSM405470", "GSM405471", "GSM405472", "GSM405473", "GSM405474", "GSM405475", "GSM405476", "GSM405477", "GSM405478", "GSM405479", "GSM405480", "GSM405481", "GSM405482", "GSM405483"], "sample_count": 284, "group_sizes": null, "group_sizes_basis": null, "platform": "8542", "taxon": "Homo sapiens", "title": "Intrinsic Gene Expression Profiles of Gliomas are a Better Predictor of Survival than Histology", "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:GSE16011 not downloaded", "asset:data:geo:GSE16011 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Pathway Enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Kaplan–Meier survival analysis was performed to estimate the effect of TRIP13 expression on overall survival (OS) and progression-free survival (PFS) from TCGA, CGGA and GSE data."}}], "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE16011"], "resolved_accessions": ["GSE16011"], "statements": ["All source data relating to this manuscript are available upon request."], "basis": "The paper names GSE16011 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:34066132", "data:geo:GSE16011"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16011"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:41Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 46727, "completion_tokens": 2786, "cached_tokens": 15616}}, "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:34066132", "type": "paper", "label": "pmid:34066132"}, {"id": "source:pmid:34066132", "type": "manuscript", "label": "PMID 34066132 full text"}, {"id": "data:geo:GSE16011", "type": "dataset", "label": "GEO GSE16011"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34066132", "type": "paper", "label": "pmid:34066132"}, {"id": "source:pmid:34066132", "type": "manuscript", "label": "PMID 34066132 full text"}, {"id": "data:geo:GSE16011", "type": "dataset", "label": "GEO GSE16011"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34066132", "type": "extraction", "used": ["source:pmid:34066132"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16011", "type": "accession_resolution", "used": ["data:geo:GSE16011"], "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:34066132", "parent_hash": "sha256:f86b4754ddc9010b3dbc0631c294da6a1b5c8690db494ad8822c568890186551", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE16011 licence not read", "asset:data:geo:GSE16011 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lower-grade glioma. We performed RT-PCR and Western blot to validate TRIP13 mRNA expression and prote"], "order_basis": "paper_text_order:815", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["grade IV was glioblastoma multiforme (GBM). RNA-seq data for specific tumor anatomic structure i", ", Table S3). All the above results suggested transcriptome-wide effects of TRIP13 on glioma. 4. Materia", "of TRIP13 Expression in Human Glioma TRIP13 transcriptome expression data for the TCGA (n = 156 gliobl"], "order_basis": "paper_text_order:3022", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["n on genes and corresponding high-resolution immunohistochemistry images, was used to examine TRIP13 expressio"], "order_basis": "paper_text_order:4180", "id": "assay:3"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["bioinfo.cnio.es/, accessed on 13 June 2020). We recruited the other two datasets to investigate TRIP13"], "order_basis": "paper_text_order:4869", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["analysis of variance"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}