Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981385", "kind": "science-record", "revision": 8, "content_hash": "sha256:a33a75ff3a7b62e017c15e0aecf60827f35f748c94b8021e4ddca8b565ffe820", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T22:42:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.", "doi": "10.1016/j.gdata.2015.12.020", "pmid": "26981385", "authors": ["Ekaterina Nevedomskaya", "Suzan Stelloo", "Henk G van der Poel", "Jeroen de Jong", "Lodewyk F A Wessels", "Andries M Bergman", "Wilbert Zwart"], "journal": "Genomics data", "year": 2016, "abstract": "Prostate cancer (PCa) is the second most common cancer in men. The Androgen Receptor (AR) is the major driver of PCa and the main target of therapy in the advanced setting. AR is a nuclear receptor that binds the chromatin and regulates transcription of genes involved in cancer cell proliferation and survival. In a study by Stelloo et al. (1) we explored prostate cancer on the level of transcriptional regulation by means of Formaldehyde-Assisted Isolation of Regulatory Elements and Chromatin Immunoprecipitation coupled with massive parallel sequencing (FAIRE-seq and ChIP-seq, respectively). We employed these data for the assessment of differences in transcriptional regulation at distinct stages of PCa progression and to construct a prognostic gene expression classifier. Genomics data includes FAIRE-seq data from normal prostate tissue as well as primary, hormone therapy resistant and metastatic PCa. Furthermore, ChIP-seq data from primary and resistant PCa were generated, along with multiple input controls. The data are publicly available through NCBI GEO database with accession number GSE65478. Here we describe the genomics and clinical data in detail and provide comparative analysis of FAIRE-seq and ChIP-seq data.", "claims": [{"id": "claim-method", "statement": "The number of peaks within 5 kb from the nearest TSS was significantly higher in FAIRE-seq data as compared to ChIP-seq data and the number of peaks further than 50 kb from a TSS was higher in ChIP-seq data than in FAIRE-seq (p < 10− 15 Fisher's exact; Fig. 2B-C).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981385", "locator": "sections[8] \"Data analysis\" paragraph 5", "quote": "The number of peaks within 5 kb from the nearest TSS was significantly higher in FAIRE-seq data as compared to ChIP-seq data and the number of peaks further than 50 kb from a TSS was higher in ChIP-seq data than in FAIRE-seq (p < 10− 15 Fisher's exact; Fig. 2B-C)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data are publicly available through NCBI GEO database with accession number GSE65478.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981385", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are publicly available through NCBI GEO database with accession number GSE65478."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Fisher’s exact test was used to compare peak distances from the nearest transcription start site, and the source data are publicly available through NCBI GEO under accession number GSE65478.", "kind": "quantitative", "target": {"value": 10.0, "unit": "p-value", "tolerance": null, "source": "The number of peaks within 5 kb from the nearest TSS was significantly higher in FAIRE-seq data as compared to ChIP-seq data and the number of peaks further than 50 kb from a TSS was higher in ChIP-seq data than in FAIRE-seq (p < 10− 15 Fisher's exact; Fig. 2B-C)."}, "evidence": [{"asset": "source:pmid:26981385", "locator": "sections[8] \"Data analysis\" paragraph 5", "quote": "The number of peaks within 5 kb from the nearest TSS was significantly higher in FAIRE-seq data as compared to ChIP-seq data and the number of peaks further than 50 kb from a TSS was higher in ChIP-seq data than in FAIRE-seq (p < 10− 15 Fisher's exact; Fig. 2B-C)."}, {"asset": "source:pmid:26981385", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are publicly available through NCBI GEO database with accession number GSE65478."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Fisher’s exact test was used to compare peak distances from the nearest transcription start site, and the source data are publicly available through NCBI GEO under accession number GSE65478.", "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:26981385"], "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. 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We employed these data for t", "y resistant and metastatic PCa. Furthermore, ChIP-seq data from primary and resistant PCa were gen", "rovide comparative analysis of FAIRE-seq and ChIP-seq data.", "node metastases (Fig. 1). Androgen Receptor ChIP-seq was carried out on four primary and three re"], "order_basis": "paper_text_order:616", "id": "assay:1"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["contingency_table", "chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The number of peaks within 5 kb from the nearest TSS was significantly higher in FAIRE-seq data as compared to ChIP-seq data and the number of peaks further than 50 kb from a TSS was higher in ChIP-seq data than in FAIRE-seq (p < 10− 15 Fisher's exact; Fig. 2B-C)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}