Construction and Validation of a Novel Eight-Gene Risk Signature to Predict the Progression and Prognosis of Bladder Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34268106", "kind": "science-record", "revision": 7, "content_hash": "sha256:4d1be9e588f84ce0518a237e150f685b63c408128c7f16e38b51e3ba8d35fee4", "created_at": "2026-11-01T15:41:43Z", "updated_at": "2026-11-01T22:04:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction and Validation of a Novel Eight-Gene Risk Signature to Predict the Progression and Prognosis of Bladder Cancer.", "doi": "10.3389/fonc.2021.632459", "pmid": "34268106", "authors": ["Ruiliang Wang", "Zongtai Zheng", "Shiyu Mao", "Wentao Zhang", "Ji Liu", "Cheng Li", "Shenghua Liu", "Xudong Yao"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "The progression from non-muscle-invasive bladder cancer (NMIBC) to muscle-invasive bladder cancer (MIBC) increases the risk of death. It is therefore important to find new relevant molecular models that will allow for effective prediction of the progression and prognosis of bladder cancer (BC). Using RNA-Sequence data of 49 BC patients in Shanghai tenth people's hospital (STPH) and weighted gene co-expression network analysis methods, a co-expression network of genes was developed and three key modules associated with malignant progression were selected. Based on the genes in three key modules, an eight-gene risk signature was established using univariate Cox regression and the Least absolute shrinkage and selection operator Cox model in The Cancer Genome Atlas Program (TCGA) and validated in validation sets. Subsequently, a nomogram based on the risk signature was constructed for prognostic prediction. The mRNA and protein expression levels of eight genes in cell lines and tissues were further investigated. The novel eight-gene risk signature was closely related to the malignant clinical features of BC and could predict the prognosis of patients in the training dataset (TCGA) and four validation sets (GSE32894, GSE13507, IMvigor210 trial, and STPH). The nomogram showed good prognostic prediction and calibration. The mRNA and protein expression levels of the eight genes were differentially expressed in cell lines and tissues. In our study, we established a novel eight-gene risk signature that could predict the progression and prognoses of BC patients.", "claims": [{"id": "claim-data-access", "statement": "Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. Requests to access the datasets should be directed to yaoxudong1967@163.com.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34268106", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. Requests to access the datasets should be directed to yaoxudong1967@163.com."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:34268106"], "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:GSE13507"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34268106", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.632459", "sha256": "sha256:325c1939fe738a7254795eb7a955ab812d6608ba40790d323f2d8b1f02bf9ca0", "bytes": 40224, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.632459", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8276675", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "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=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. Requests to access the datasets should be directed to yaoxudong1967@163.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. 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IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. Requests to access the datasets should be directed to yaoxudong1967@163.com.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE32894", "GSE13507"], "resolved_accessions": ["GSE32894", "GSE13507"], "statements": ["Public data that support the findings of this study are openly available in TCGA (http://cancergenome.nih.gov/), NCBI GEO dataset GSE32894 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32894) and GSE13507 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507). IMvigor210 with immunotherapy data and clinical information were obtained from the IMvigor210CoreBiologies R package. The processed data required to reproduce these findings cannot be shared at this time as the data also form part of an ongoing study. Requests to access the datasets should be directed to yaoxudong1967@163.com."], "basis": "The paper names GSE32894, GSE13507 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34268106", "data:geo:GSE13507"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13507"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:28Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31993, "completion_tokens": 2697, "cached_tokens": 528}}, "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:34268106", "type": "paper", "label": "pmid:34268106"}, {"id": "source:pmid:34268106", "type": "manuscript", "label": "PMID 34268106 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34268106", "type": "paper", "label": "pmid:34268106"}, {"id": "source:pmid:34268106", "type": "manuscript", "label": "PMID 34268106 full text"}, {"id": "data:geo:GSE13507", "type": "dataset", "label": "GEO GSE13507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34268106", "type": "extraction", "used": ["source:pmid:34268106"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13507", "type": "accession_resolution", "used": ["data:geo:GSE13507"], "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:34268106", "parent_hash": "sha256:4ffa5820d07b99a03024a7249a59ec9f8807977376fc53fcbd98262b5bd3a3dd", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE13507 licence not read", "asset:data:geo:GSE13507 not downloaded", "asset:data:geo:GSE32894 licence not read", "asset:data:geo:GSE32894 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"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": ["Materials and Methods Clinical Samples and RNA-Sequencing A total of 49 BC patients (35 NMIBC and 14 M", "hai Tenth People’s Hospital. The workflow of RNA-Seq was performed as described in an earlier art"], "order_basis": "paper_text_order:1703", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n in Supplement Table 1 . The representative immunohistochemistry (IHC) of genes in both normal human bladder", "1 . 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