{"id":"pdc-cptac-ccrcc-discovery-study","title":"CPTAC CCRCC Discovery Study","short_title":"PDC000471","aliases":["CPTAC CCRCC Discovery Study - DIA Proteome","CPTAC CCRCC Discovery Study - Intact Glycoproteome","CPTAC CCRCC Discovery Study - Phosphoproteome","CPTAC CCRCC Discovery Study - Proteome"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000471","url":"https://pdc.cancer.gov/pdc/study/PDC000471","is_primary":true,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000128","url":"https://pdc.cancer.gov/pdc/study/PDC000128","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000200","url":"https://pdc.cancer.gov/pdc/study/PDC000200","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"pdc_study_id","value":"PDC000127","url":"https://pdc.cancer.gov/pdc/study/PDC000127","is_primary":false,"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"repository":{"name":"NCI Proteomic Data Commons","short_name":"PDC","url":"https://pdc.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"Clinical Proteomic Tumor Analysis Consortium","program_url":"https://pdc.cancer.gov/pdc/browse","nci_program":"Clinical Proteomic Tumor Analysis Consortium","generating_institutions":[],"data_generation_funding_role":"generation","version":null,"release_date":"2023-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000471","cancer_types":[],"primary_sites":[],"subject":{"scope":"title_derived","tissues":["KIDNEY"],"evidence":[{"method":"derived","source_url":null,"source_label":"Dataset title","retrieved_at":null,"snippet":null,"locator":"title: CPTAC CCRCC Discovery Study","confidence":"low","reviewer":null,"reviewed_at":null,"note":"Subject derived from the title because the repository did not state one. It is available for browsing but cannot admit this record to a topic shortlist."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":124,"n_samples":null,"n_aliquots":818,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[]},"evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"glycoproteome","label":"Glycoproteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":124,"n_samples":208,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"phosphoproteome","label":"Phosphoproteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":124,"n_samples":208,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"proteome","label":"Proteome mass spectrometry (Label Free / DIA)","platform":"Label Free","n_cases":110,"n_samples":194,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"proteome","label":"Proteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":124,"n_samples":208,"n_files":null,"data_levels":["raw","peptide/protein matrix"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[],"longitudinal":{"has_followup":null,"has_survival_endpoint":null,"survival_endpoints":[],"median_followup_months":null,"max_followup_months":null,"n_cases_with_followup":null,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":null,"response_criteria":[],"evidence":[]},"access":{"tier":"open","open_components":["4 analytical fraction studies"],"controlled_components":[],"mechanism":"Direct download from the PDC portal or its API; no account required","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the PDC study identifier and the study's primary publication; PDC asks that the consortium be acknowledged.","license":"Open access under the PDC data use terms","publication_policy_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","evidence":[{"method":"api","source_url":"https://proteomic.datacommons.cancer.gov/graphql","source_label":"PDC GraphQL allPrograms","retrieved_at":"2026-09-18T02:36:15.354973Z","snippet":null,"locator":"4 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[],"inappropriate_uses":[],"primary_publications":[],"reuse":[{"publication":{"pmid":"39254081","pmcid":"PMC13142904","doi":"10.1021/acs.jproteome.4c00294","title":"Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst.","journal":"Journal of proteome research","year":2024,"authors_short":"Hsiao et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39254081/","is_open_access":false,"citation_count":136,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["deng y","hsiao y","nesvizhskii a","schittenhelm r","steele j","valipour k","zhang h"],"nci_funded_reuse":true,"linked_grants":["U24CA210967"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"36189312","pmcid":"PMC9523360","doi":"10.3389/fimmu.2022.975057","title":"Telomere-related gene risk model for prognosis and drug treatment efficiency prediction in kidney cancer.","journal":"Frontiers in immunology","year":2022,"authors_short":"Li et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36189312/","is_open_access":true,"citation_count":52,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["jia z","ning x","yang j"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"37989747","pmcid":"PMC10663509","doi":"10.1038/s41467-023-43378-w","title":"SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer.","journal":"Nature communications","year":2023,"authors_short":"Rao et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37989747/","is_open_access":true,"citation_count":42,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, SUPPL","author_keys":["ding x","gao w","liu c","rao h","wang a","zhou p"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000471\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"37680718","pmcid":"PMC10482042","doi":"10.3389/fphar.2023.1213891","title":"Identification and validation of SERPINE1 as a prognostic and immunological biomarker in pan-cancer and in ccRCC.","journal":"Frontiers in pharmacology","year":2023,"authors_short":"Li et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37680718/","is_open_access":true,"citation_count":35,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["gao l","wang m"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"37074911","pmcid":"PMC10247542","doi":"10.1016/j.celrep.2023.112409","title":"Integrated glycoproteomic characterization of clear cell renal cell carcinoma.","journal":"Cell reports","year":2023,"authors_short":"Lih et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37074911/","is_open_access":false,"citation_count":34,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["cho k","lih t","schnaubelt m","zhang h"],"nci_funded_reuse":true,"linked_grants":["U24CA271079","U24CA210985"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38759626","pmcid":"PMC11129317","doi":"10.1016/j.molcel.2024.04.012","title":"Arginine deprivation enriches lung cancer proteomes with cysteine by inducing arginine-to-cysteine substitutants.","journal":"Molecular cell","year":2024,"authors_short":"Yang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38759626/","is_open_access":true,"citation_count":28,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["agami r","berkers c","bleijerveld o","feng x","jacobs j","montenegro n","paniagua i","pataskar a","yang c","zaal e"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38504097","pmcid":"PMC10950894","doi":"10.1038/s41467-024-46132-y","title":"Genetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets.","journal":"Nature communications","year":2024,"authors_short":"Xu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38504097/","is_open_access":true,"citation_count":21,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["antczak a","bogdanski p","charchar f","danser a","denniff m","diwadkar a","dormer j","drzal m","eales j","guzik t","human k","keavney b","khunsriraksakul c","król r","lay a","liu d","maan a","markus h","matías-garcía p","morris a","prestes p","regan j","rempega g","rubin s","ryszawy j","saluja s","samani n","scannali d","szulinska m","talavera d","tomaszewski m","walczak m","waldenberger m","wang l","woolf a","wystrychowski w","zukowska-szczechowska e","zywiec j"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38098449","pmcid":"PMC10722140","doi":"10.1158/0008-5472.can-23-0604","title":"Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.","journal":"Cancer research","year":2023,"authors_short":"Wu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38098449/","is_open_access":true,"citation_count":17,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, METHODS","author_keys":["chen f","chen s","chuang j","davies s","ding l","ding x","evrard y","fields r","gould a","govindan r","herndon j","hoog j","hsieh j","koh m","lal p","lim k","liu d","liu r","lum d","mashl r","meric-bernstam f","moscow j","mudd j","primeau t","sato k","shinkle a","sun h","wang y","welm a","welm b","wendl m","wyczalkowski m","yang x","zhang h","zhao y"],"nci_funded_reuse":true,"linked_grants":["U54CA224083","U54CA224076","R01CA260112","P30CA091842","P30CA042014"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000471\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"37517589","pmcid":"PMC10494184","doi":"10.1016/j.mcpro.2023.100626","title":"Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics.","journal":"Molecular & cellular proteomics : MCP","year":2023,"authors_short":"Wang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37517589/","is_open_access":true,"citation_count":15,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"METHODS","author_keys":["bullen j","d'angelo g","d'anna r","hurt e","lai z","przybyla a","sidders b","sung m","wang j","wilson m","zhong w"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=METHODS:\"PDC000471\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in METHODS","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]},{"publication":{"pmid":"38822145","pmcid":"PMC11263541","doi":"10.1038/s41416-024-02725-4","title":"PDZK1 confers sensitivity to sunitinib in clear cell renal cell carcinoma by suppressing the PDGFR-β pathway.","journal":"British journal of cancer","year":2024,"authors_short":"Wang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38822145/","is_open_access":false,"citation_count":12,"evidence":[]},"tier":"t3_analyzed","kind":"secondary_analysis","independent_of_generators":null,"what_they_analyzed":null,"what_they_found":null,"methods_summary":null,"modalities_used":[],"accession_snippet":null,"accession_locator":"DATA_AVAILABILITY, SUPPL","author_keys":["bai t","cao x","feng d","liu h","qin q","song r","wang h","wang s","yang x","yang y","zhang l"],"nci_funded_reuse":false,"linked_grants":[],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000471\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:25:45.096633Z","snippet":null,"locator":"accession \"PDC000471\" indexed in DATA_AVAILABILITY","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Search strategy epmc-sectioned-v1. Section placement is used to grade the strength of reuse evidence, not merely to confirm a citation."}]}],"reuse_metrics":{"n_candidates_screened":4,"n_by_tier":{"t3_analyzed":4,"t2_declared":2,"t1_accession":0,"t0_mention":0},"n_by_tier_raw":{"t3_analyzed":4,"t2_declared":2,"t1_accession":0,"t0_mention":0},"accession_precision":{"token":"PDC000128","query":"METHODS:\"PDC000128\"","strategy_id":"epmc-literal-precision-v1","needs_correction":false,"precision":1.0,"precision_low":1.0,"precision_high":1.0,"n_sampled":0,"n_checked":0,"n_literal":0,"note":"This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":true,"n_verified_reuse":4,"n_reuse_examined":45,"n_independent_reuse":0,"n_nci_funded_reuse":3,"first_reuse_year":2022,"latest_reuse_year":2024,"years_since_release":3.72,"expected_reuse":11.66,"reuse_gap_index":-1.34,"reuse_gap_percentile":20.5,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.706377Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC section-scoped hit counts","retrieved_at":"2026-09-20T18:07:48.706377Z","snippet":null,"locator":"tokens: PDC000471, PDC000128, PDC000200; queries: METHODS:\"PDC000128\"; DATA_AVAILABILITY:\"PDC000471\"; ACCESSION_ID:\"PDC000471\"; REF:\"PDC000471\"","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Index strategy epmc-index-v3. Every dataset is measured with the same single section field per tier, so the counts are comparable; the per-tier value is the largest across the dataset's own accessions, excluding any accession shared with other datasets in the corpus. This accession is a single indexed term, so Europe PMC matches it exactly and the hit count needs no correction."},{"method":"derived","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search","source_label":"Europe PMC first-reference dating","retrieved_at":"2026-09-20T18:14:10.930528Z","snippet":null,"locator":"first referenced in 2023 (METHODS section)","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Availability dated from the literature (epmc-first-reference-v2) rather than from repository file timestamps, which record re-harmonization. This is a lower bound on availability."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index -1.34)."],"index_value":-1.34,"percentile":20.5,"comparator_set":"132 datasets in this corpus with a citable accession and sufficient metadata","evidence":[{"method":"derived","source_url":null,"source_label":"Reuse Gap Index (rgi-huber-v2)","retrieved_at":"2026-09-21T02:11:22.976067Z","snippet":null,"locator":"Huber robust regression of log2(analyzing articles + 1) on cohort size, years available, modality breadth and access tier","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Model, covariates and coefficients are published with the dataset export so the label can be recomputed or contested."}]},"grants":[{"core_project_num":"U24CA210967","project_num":null,"title":"University of Michigan Proteogenomics Data Analysis Center","pi_names":["ARUL M CHINNAIYAN","Saravana M Dhanasekaran","Alexey I Nesvizhskii"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":4075837,"org_name":"UNIVERSITY OF MICHIGAN AT ANN ARBOR","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210967","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 39254081 reported under U24CA210967","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA271079","project_num":null,"title":"Proteogenomic Characterization of Tumor Tissues and Preclinical Models with High Precision","pi_names":["DANIEL Wanyui CHAN","Hui Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":6618085,"org_name":"JOHNS HOPKINS UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA271079","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 37074911 reported under U24CA271079","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U24CA210985","project_num":null,"title":"The Comprehensive Proteome Characterization Center at Johns Hopkins: High Precision Discovery and Confirmation of Genoproteomic Targets","pi_names":["DANIEL Wanyui CHAN","ZHEN ZHANG","Hui Zhang"],"agency_ic":"NCI","activity_code":"U24","fiscal_years":[2016,2017,2018,2019,2020],"award_amount_usd":5267994,"org_name":"JOHNS HOPKINS UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U24CA210985","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 37074911 reported under U24CA210985","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U54CA224083","project_num":null,"title":"Bioinformatics Core","pi_names":["Li Ding","Cynthia X Ma","Kian-Huat Lim","Brian Andrew Van Tine","FENG CHEN","Ramaswamy Govindan","JOHN A. OLSON","Ryan C Fields","Shunqiang Li","Andrea Wang-Gillam","John F. Dipersio"],"agency_ic":"NCI","activity_code":"U54","fiscal_years":[2017,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":20397875,"org_name":"WASHINGTON UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U54CA224083","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 38098449 reported under U54CA224083","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"U54CA224076","project_num":null,"title":"Administrative Core","pi_names":["Alana L. Welm","Gabor T Marth","Michael T. Lewis","Bryan E. Welm","Kenneth Michael Boucher"],"agency_ic":"NCI","activity_code":"U54","fiscal_years":[2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":24765874,"org_name":"UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U54CA224076","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 38098449 reported under U54CA224076","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"R01CA260112","project_num":null,"title":"Impact of cancer predisposition on oncogenic process, microenvironment, and treatment","pi_names":["FENG CHEN","Li Ding"],"agency_ic":"NCI","activity_code":"R01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":2352654,"org_name":"WASHINGTON UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=R01CA260112","role":"reuse","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 38098449 reported under R01CA260112","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P30CA091842","project_num":null,"title":"Tissue Procurement Core","pi_names":["Mark A. Watson","EDUARDO ROSA-MOLINAR","Adetunji T Toriola","TIMOTHY J. EBERLEIN","Amanda Fishback Cashen","Xiaoxia Cui","Jason Weber","AIMEE S JAMES","Jingqin Luo","Shawn Shafer","MARILYN J SIEGEL","KATHLEEN C SHEEHAN","Young Ah Goo","Grant Anthony Challen","David G DeNardo","Roberta Faccio","Christopher A Maher","Bettina F. Drake","ALBERT M LAI","Joel Richard Garbow","GEOFFREY L UY","FARROKH DEHDASHTI","MEAGAN JACOBY","JEFFREY F. MOLEY","Jeff M. Michalski","ROBERT DAVID SCHREIBER","MATTHEW W. KREUTER","Timothy J. Ley","BARRY A. SIEGEL","Daniel C Link","REID TOWNSEND","RAKESH NAGARAJAN","ROBERT MYERSON","David M Ornitz","HELEN M PIWNICA-WORMS","MICHAEL J. WELCH","MATTHEW J ELLIS","JOSEPH J. H. ACKERMAN","TIMOTHY A GRAUBERT","DONNA B JEFFE","J. Philip MILLER","NANCY L BARTLETT","Paul Joseph Goodfellow","HOWARD L MCLEOD","JOEL PICUS","Edwin B Fisher","BARBARA A ZEHNBAUER","ROBERT REID TOWNSEND","MICHAEL J WELCH","BRIAN SPRINGER"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[2001,2002,2003,2004,2005,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":223241311,"org_name":"WASHINGTON UNIVERSITY","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA091842","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 38098449 reported under P30CA091842","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]},{"core_project_num":"P30CA042014","project_num":null,"title":"Cancer Biostatistics (CB)","pi_names":["Yian Ann Chen","MARTIN MCMAHON","KATHARINE S ULLMAN","Howard Colman","CORNELIA M ULRICH","Max Loveless","BRIAN DALLEY","Gary Christopher Fillmore","Sheri L Holmen","Rachel M. Ceballos","Neeraj Agarwal","NICOLA J. CAMP","Whitney F Maxwell","Andrew Ronald Post","Jared P Rutter","Jennifer Anne Doherty","Donald E Ayer","KATHLEEN H MOONEY","Wallace Lovell Akerley","Kenneth Michael Boucher","Tracy Onega","Theresa Louise Werner","Scott Lloyd","Wendy K Kohlmann","Ken R Smith","Jason Gertz","David K Gaffney","David W Wetter","Trudy Gale Oliver","Alana L. Welm","BRADLEY R. CAIRNS","Eric Lee Snyder","Mary C. Beckerle","EVIN GULBAHCE","John M Hoffman","DOUGLAS GROSSMAN","SAMIR COURDY","Lisa Cannon Albright","Anita Y. Kinney","CAROL SWEENEY","CHRISTOPHER K RODESCH","GERALDINE P MINEAU","Barbara J Graves","CHAD C NELSON","David Gaffney","RANDALL Walter BURT","KURT H ALBERTINE","Stephen M Prescott","Alexander Tsodikov","RICHARD H WHEELER","ROBERT W SCHACKMANN","JAMES A MC CLOSKEY","Michelle M Adams","CHRISTINE LASALLE","ANDREI Y YAKOVLEV","Margaret Roberson","WAYNE FRANCIS GREEN","Aurelia Meloni-Ehrig","MARK LEPPERT","H. Steven WILEY","Patrick G. Beatty","GLENN DOWNES PRESTWICH","SAUNDRA S BUYS","DAVID G. MYSZKA","MICHAEL J CINKOSKY","Thomas M McIntyre","PETER M HEILBRUN","RAYMOND L WARTERS","BRADLEY D PRESTON","RAYMOND L WHITE","DARRYL R DAVIS","ARTHUR R BROTHMAN","ROBERT B WEISS","MARLENE J EGGER","ROBERT WEISS","JAMES A. MCCLOSKEY","SAUNDRA BUYS","MARK F LEPPERT","WAYNE F GREEN","ROBERT SCHACKMANN","DWIGHT T JANERICH","J. ROBERT STEWART","ROBERT M STEWART"],"agency_ic":"NCI","activity_code":"P30","fiscal_years":[1986,1987,1988,1989,1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,2000,2001,2002,2003,2004,2005,2006,2007,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024,2025,2026],"award_amount_usd":140586331,"org_name":"UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=P30CA042014","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-20T17:50:59.017228Z","snippet":null,"locator":"PMID 38098449 reported under P30CA042014","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Funding role inferred from whether the award appears on the dataset's own publication or on a downstream study."}]}],"access_steps":[{"order":1,"action":"Open the study in the PDC portal","detail":"Proteomic data are released open; the portal's use guidelines still apply. This record spans 4 PDC studies; repeat for each.","url":"https://pdc.cancer.gov/pdc/study/PDC000471","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000471","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433520Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Accept the data use guidelines and download","detail":"The portal asks for acknowledgement and citation, not a data access request.","url":"https://pdc.cancer.gov/pdc/data-use-guidelines","requires":[],"est_time":"minutes to hours, by study size","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/data-use-guidelines","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433522Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Resolve the study UUID, then fetch the file manifest","detail":"filesPerStudy keys on the study UUID, not on PDC000471: called with the pdc_study_id it returns the right number of rows with every column null. Resolve the UUID first and pass the terms acknowledgement.","url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nimport requests\nAPI = \"https://proteomic.datacommons.cancer.gov/graphql\"\n\ndef gql(query, **variables):\n    r = requests.post(API, json={\"query\": query, \"variables\": variables}, timeout=180)\n    r.raise_for_status()\n    body = r.json()\n    if body.get(\"errors\"):\n        raise RuntimeError(body[\"errors\"][0][\"message\"])\n    return body[\"data\"]\n\nstudy = gql('query($id:String!){ study(pdc_study_id:$id acceptDUA:true){ study_id } }',\n            id=\"PDC000471\")[\"study\"][0]\nfiles = gql('query($sid:String!){ filesPerStudy(study_id:$sid acceptDUA:true)'\n            '{ file_id file_name file_size } }', sid=study[\"study_id\"])[\"filesPerStudy\"]\nprint(len(files), \"files\")\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/data-dictionary/publicapi-documentation/","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.433525Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[],"agent_package":{"json_url":"/data/datasets/pdc-cptac-ccrcc-discovery-study.json","jsonld_url":"/data/jsonld/pdc-cptac-ccrcc-discovery-study.jsonld","croissant_url":"/data/croissant/pdc-cptac-ccrcc-discovery-study.json","instructions_url":"/data/agent/pdc-cptac-ccrcc-discovery-study.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":false,"completeness_score":26.8,"tags":["pdc","proteogenomics","rare-modality","glycoproteome"],"search_text":null}