{"id":"pdc-prospective-colon-pnnl-proteome-qeplus","title":"Prospective Colon PNNL Proteome Qeplus","short_title":"PDC000116","aliases":["Prospective Colon PNNL Proteome Qeplus"],"summary":null,"one_liner":null,"identifiers":[{"scheme":"pdc_study_id","value":"PDC000116","url":"https://pdc.cancer.gov/pdc/study/PDC000116","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":"1 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":"2022-01-01","last_upstream_update":null,"retrieved_at":"2026-09-18T02:36:15.354973Z","landing_page_url":"https://pdc.cancer.gov/pdc/study/PDC000116","cancer_types":[],"primary_sites":[],"subject":{"scope":"title_derived","tissues":["BOWEL"],"evidence":[{"method":"derived","source_url":null,"source_label":"Dataset title","retrieved_at":null,"snippet":null,"locator":"title: Prospective Colon PNNL Proteome Qeplus","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":102,"n_samples":null,"n_aliquots":198,"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":"1 fraction studies grouped by cohort name","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"proteome","label":"Proteome mass spectrometry (TMT10 / DDA)","platform":"TMT10","n_cases":102,"n_samples":198,"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":"1 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":["1 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":"1 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":"36639644","pmcid":"PMC9838026","doi":"10.1186/s40170-022-00301-z","title":"Arginase-1 inhibition reduces migration ability and metastatic colonization of colon cancer cells.","journal":"Cancer & metabolism","year":2023,"authors_short":"Wang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36639644/","is_open_access":true,"citation_count":23,"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":["homma s","kimura s","kitamura h","miyagi y","nakamoto h","shen w","shichi s","sugiyama k","taketomi a","toyoshima y","wang x","xiang h"],"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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"38855188","pmcid":"PMC11155395","doi":"10.7150/thno.95485","title":"LINC00982-encoded protein PRDM16-DT regulates CHEK2 splicing to suppress colorectal cancer metastasis and chemoresistance.","journal":"Theranostics","year":2024,"authors_short":"Hu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38855188/","is_open_access":true,"citation_count":18,"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":"RESULTS","author_keys":["chen q","han j","han l","tan 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=RESULTS:\"PDC000116\"","source_label":"Europe PMC section search (RESULTS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" indexed in RESULTS","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":"36396045","pmcid":"PMC10491971","doi":"10.1016/j.jare.2022.11.006","title":"Targeting ARF1-IQGAP1 interaction to suppress colorectal cancer metastasis and vemurafenib resistance.","journal":"Journal of advanced research","year":2023,"authors_short":"Hu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36396045/","is_open_access":true,"citation_count":18,"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 g","pan y","wang y"],"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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"39865075","pmcid":"PMC11770092","doi":"10.1038/s41392-025-02128-8","title":"The cryptic lncRNA-encoded microprotein TPM3P9 drives oncogenic RNA splicing and tumorigenesis.","journal":"Signal transduction and targeted therapy","year":2025,"authors_short":"Meng et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39865075/","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":"METHODS","author_keys":["cao y","liu d","meng k","pan y","shen h","shi f","shi x","wen n","yuan x","zhang c","zheng d"],"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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"38724493","pmcid":"PMC11082183","doi":"10.1038/s41467-024-47957-3","title":"Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.","journal":"Nature communications","year":2024,"authors_short":"Rosenberger et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/38724493/","is_open_access":true,"citation_count":16,"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":["califano a","griffin a","honig b","karan c","kerwin p","liu y","murray d","pampou s","rosenberger g","subramaniam p","turunen m"],"nci_funded_reuse":true,"linked_grants":["U54CA274506","U54CA209997","U01CA272610"],"adjudicated_by":null,"adjudicated_at":null,"evidence":[{"method":"fulltext","source_url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=DATA_AVAILABILITY:\"PDC000116\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"36531007","pmcid":"PMC9753687","doi":"10.3389/fonc.2022.1035188","title":"Inflammation-related citrullination of matrisome proteins in human cancer.","journal":"Frontiers in oncology","year":2022,"authors_short":"Rappu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36531007/","is_open_access":true,"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":"METHODS","author_keys":["heino j","rappu p","siljamäki e","suwal u"],"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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"39775839","pmcid":"PMC11702362","doi":"10.1093/gigascience/giae113","title":"Mutation impact on mRNA versus protein expression across human cancers.","journal":"GigaScience","year":2025,"authors_short":"Liu et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/39775839/","is_open_access":true,"citation_count":9,"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":["elmas a","huang k","liu y"],"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:\"PDC000116\"","source_label":"Europe PMC section search (DATA_AVAILABILITY)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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":"36428765","pmcid":"PMC9688665","doi":"10.3390/cancers14225674","title":"Pan-Cancer Analysis Identifies Tumor Cell Surface Targets for CAR-T Cell Therapies and Antibody Drug Conjugates.","journal":"Cancers","year":2022,"authors_short":"Li et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/36428765/","is_open_access":true,"citation_count":9,"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":"TABLE","author_keys":["chen w","liu l","wang j","you w","zhang w","zhou j","zhou 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=TABLE:\"PDC000116\"","source_label":"Europe PMC section search (TABLE)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" indexed in TABLE","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":"37257561","pmcid":"PMC10331287","doi":"10.1016/j.jlr.2023.100393","title":"Equivalent carbon number-based targeted odd-chain fatty acyl lipidomics reveals triacylglycerol profiling in clinical colon cancer.","journal":"Journal of lipid research","year":2023,"authors_short":"Zhang et al.","n_authors":null,"url":"https://pubmed.ncbi.nlm.nih.gov/37257561/","is_open_access":true,"citation_count":8,"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":["chen y","lei j","wang j","yang s","zhang j","zhao h","zhou y"],"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:\"PDC000116\"","source_label":"Europe PMC section search (METHODS)","retrieved_at":"2026-09-18T03:29:19.561574Z","snippet":null,"locator":"accession \"PDC000116\" 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."}]}],"reuse_metrics":{"n_candidates_screened":19,"n_by_tier":{"t3_analyzed":19,"t2_declared":8,"t1_accession":0,"t0_mention":1},"n_by_tier_raw":{"t3_analyzed":19,"t2_declared":8,"t1_accession":0,"t0_mention":1},"accession_precision":{"token":"PDC000116","query":"METHODS:\"PDC000116\"","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":19,"n_reuse_examined":29,"n_independent_reuse":0,"n_nci_funded_reuse":1,"first_reuse_year":2022,"latest_reuse_year":2025,"years_since_release":4.72,"expected_reuse":4.04,"reuse_gap_index":1.987,"reuse_gap_percentile":92.4,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:48.904258Z","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":"2026-09-20T18:07:48.904258Z","snippet":null,"locator":"tokens: PDC000116; queries: METHODS:\"PDC000116\"; DATA_AVAILABILITY:\"PDC000116\"; ACCESSION_ID:\"PDC000116\"; INTRO:\"PDC000116\"","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":"2026-09-20T18:15:55.027949Z","snippet":null,"locator":"first referenced in 2022 (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."},{"method":"derived","source_url":null,"source_label":"Marker-paper inference withdrawn","retrieved_at":"2026-09-20T18:18:47.942860Z","snippet":null,"locator":"PMID 35264796 was nominated for 3 datasets","confidence":"high","reviewer":null,"reviewed_at":null,"note":"A marker paper describes one cohort. This article was inferred as the marker paper for several datasets at once, which means the inference is wrong for all but one of them and we cannot tell which, so no marker paper is claimed for this record."}]},"underexplored":{"is_underexplored":false,"basis":["Reuse is within the expected range for comparable datasets (index +1.99)."],"index_value":1.987,"percentile":92.4,"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":"U54CA274506","project_num":null,"title":"Outreach Core","pi_names":["DIANA MURRAY","ANDREA CALIFANO","BARRY H HONIG","Peter Alan Sims","Benjamin Izar"],"agency_ic":"NCI","activity_code":"U54","fiscal_years":[2023,2024,2025,2026],"award_amount_usd":14616994,"org_name":"COLUMBIA UNIVERSITY HEALTH SCIENCES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U54CA274506","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:29:19.661219Z","snippet":null,"locator":"PMID 38724493 reported under U54CA274506","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":"U54CA209997","project_num":null,"title":"Structural and Functional Biology-based analysis of non-oncogene cancer dependencies","pi_names":["ANDREA CALIFANO","BARRY H HONIG","Raul Rabadan","Peter Alan Sims","DIANA MURRAY"],"agency_ic":"NCI","activity_code":"U54","fiscal_years":[2016,2017,2018,2019,2020,2021],"award_amount_usd":21167491,"org_name":"COLUMBIA UNIVERSITY HEALTH SCIENCES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U54CA209997","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:29:19.661219Z","snippet":null,"locator":"PMID 38724493 reported under U54CA209997","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":"U01CA272610","project_num":null,"title":"Elucidating and Targeting tumor dependencies and drug resistance determinants at the single cell level","pi_names":["ANDREA CALIFANO"],"agency_ic":"NCI","activity_code":"U01","fiscal_years":[2022,2023,2024,2025,2026],"award_amount_usd":4816581,"org_name":"COLUMBIA UNIVERSITY HEALTH SCIENCES","reporter_url":"https://reporter.nih.gov/search/results?text_criteria=U01CA272610","role":"infrastructure","evidence":[{"method":"api","source_url":"https://api.reporter.nih.gov/v2/publications/search","source_label":"NIH RePORTER","retrieved_at":"2026-09-18T03:29:19.661219Z","snippet":null,"locator":"PMID 38724493 reported under U01CA272610","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.","url":"https://pdc.cancer.gov/pdc/study/PDC000116","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://pdc.cancer.gov/pdc/study/PDC000116","source_label":"PDC access documentation","retrieved_at":"2026-09-21T12:30:59.434873Z","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":"2026-09-21T12:30:59.434875Z","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 PDC000116: 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=\"PDC000116\")[\"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":"2026-09-21T12:30:59.434877Z","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-prospective-colon-pnnl-proteome-qeplus.json","jsonld_url":"/data/jsonld/pdc-prospective-colon-pnnl-proteome-qeplus.jsonld","croissant_url":"/data/croissant/pdc-prospective-colon-pnnl-proteome-qeplus.json","instructions_url":"/data/agent/pdc-prospective-colon-pnnl-proteome-qeplus.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"],"search_text":null}