← All .science files
pmid:31506496
Aberrant Regulation of RAD51 Promotes Resistance of Neoadjuvant Endocrine Therapy in ER-positive Breast Cancer.
Yan Jia · Yueshuai Song · Guolei Dong · Chunfang Hao · Weipeng Zhao · Shufen Li · Zhongsheng Tong
Scientific reports · 2019 doi:10.1038/s41598-019-49373-w
Paper
complete
Experiment
partial
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 · 7 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 · 1 item
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 218 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 items
[0] array · 2 items
[1] array · 3 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 3 items
gaps array · 2 items
analysis object · 4 fields
methods array · 3 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
evidence object · 3 fields
[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
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 · 0 items
missing_operations array · 1 item
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 · 0 items
assets array · 3 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
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 · 8 items
assays array · 2 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 · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31506496", "kind": "science-record", "revision": 8, "content_hash": "sha256:dbf4494eb322b18604e8c28ab6705b22cdc0b4c40cc80bec65fa1960fc82b604", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:44:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Aberrant Regulation of RAD51 Promotes Resistance of Neoadjuvant Endocrine Therapy in ER-positive Breast Cancer.", "doi": "10.1038/s41598-019-49373-w", "pmid": "31506496", "authors": ["Yan Jia", "Yueshuai Song", "Guolei Dong", "Chunfang Hao", "Weipeng Zhao", "Shufen Li", "Zhongsheng Tong"], "journal": "Scientific reports", "year": 2019, "abstract": "Breast cancer is one of the most common malignant cancers affecting females. Estrogen receptor (ER)-positive breast cancer is responsive to endocrine therapy. Although current therapies offer favorable prospects for improving survival, the development of resistance remains a severe problem. In this study, we explored the resistance mechanisms of ER-positive breast cancer to neoadjuvant endocrine therapy. Microarray data of GSE87411 contained 109 pairs of samples from Z1031 trial, including untreated samples and post-treated samples with neoadjuvant aromatase inhibitor (AI) therapy. The differentially expressed genes (DEGs) were obtained from two different comparisons: untreated samples versus post-treated samples with AIs, and post-treated samples sensitive versus resistant to AIs. Multiple bioinformatic methods were applied to evaluate biological function, protein-protein network and potential binding between target protein and aromatase inhibitor. Then, regulation of gene expression, DNA methylation and clinicopathological factors of breast cancer were further analyzed with TCGA data. From GSE87411 dataset, 30 overlapped DEGs were identified. Cell division was found to be the main function of overlapped DEGs by functional enrichment and gene ontology (GO) analysis. RAD51 recombinase (RAD51), a key protein of homologous recombination, was detected to interact with BReast CAncer genes 2 (BRCA2). Moreover, according to the docking simulation, RAD51 might potentially bind to AIs. Overexpressed RAD51 was associated with hypermethylation of BRCA2, resistance to AIs and poor overall survival of patients with ER-positive breast cancer. Furthermore, RAD51 was found to be a better indicator than MKI67 for predicting resistance in neoadjuvant setting. The results indicated that methylation of BRCA2 led to incomplete suppression on RAD51, which caused an increased expression of RAD51, subsequently AI-resistance and poor prognosis in ER-positive breast cancer. RAD51 could be a new candidate used as a predicative marker and therapeutic target in neoadjuvant endocrine treatment.", "claims": [{"id": "claim-method", "statement": "The Wilcoxon rank-sum and Fisher exact tests were used to analyze the association between gene expression and clinical characteristics. Pearson correlation was applied to calculate different parameters in terms of correlation. T test was performed for the evaluation of differences between groups. The criteria of P value < 0.05 was determined to be significantly different.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31506496", "locator": "sections[6] \"Statistical analysis\" paragraph 2", "quote": "The Wilcoxon rank-sum and Fisher exact tests were used to analyze the association between gene expression and clinical characteristics. Pearson correlation was applied to calculate different parameters in terms of correlation. T test was performed for the evaluation of differences between groups. The criteria of P value < 0.05 was determined to be significantly different."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data is provided in the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31506496", "locator": "sections[19] \"notes\" paragraph 1", "quote": "All data is provided in the manuscript."}], "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:31506496"], "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:GSE87411"], "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:GSE87411"], "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:31506496", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-019-49373-w", "sha256": "sha256:21d2d54839458ce2dd1c35b9f7513e1cb3042aa8e0edb1c393b2ff36b60850fc", "bytes": 36428, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-019-49373-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6736845", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE87411", "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=GSE87411", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87411", "version": null, "note": "All data is provided in the manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data is provided in the manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2330297", "GSM2330298", "GSM2330299", "GSM2330300", "GSM2330301", "GSM2330302", "GSM2330303", "GSM2330304", "GSM2330305", "GSM2330306", "GSM2330307", "GSM2330308", "GSM2330309", "GSM2330310", "GSM2330311", "GSM2330312", "GSM2330313", "GSM2330314", "GSM2330315", "GSM2330316", "GSM2330317", "GSM2330318", "GSM2330319", "GSM2330320", "GSM2330321", "GSM2330322", "GSM2330323", "GSM2330324", "GSM2330325", "GSM2330326", "GSM2330327", "GSM2330328", "GSM2330329", "GSM2330330", "GSM2330331", "GSM2330332", "GSM2330333", "GSM2330334", "GSM2330335", "GSM2330336", "GSM2330337", "GSM2330338", "GSM2330339", "GSM2330340", "GSM2330341", "GSM2330342", "GSM2330343", "GSM2330344", "GSM2330345", "GSM2330346", "GSM2330347", "GSM2330348", "GSM2330349", "GSM2330350", "GSM2330351", "GSM2330352", "GSM2330353", "GSM2330354", "GSM2330355", "GSM2330356", "GSM2330357", "GSM2330358", "GSM2330359", "GSM2330360", "GSM2330361", "GSM2330362", "GSM2330363", "GSM2330364", "GSM2330365", "GSM2330366", "GSM2330367", "GSM2330368", "GSM2330369", "GSM2330370", "GSM2330371", "GSM2330372", "GSM2330373", "GSM2330374", "GSM2330375", "GSM2330376", "GSM2330377", "GSM2330378", "GSM2330379", "GSM2330380", "GSM2330381", "GSM2330382", "GSM2330383", "GSM2330384", "GSM2330385", "GSM2330386", "GSM2330387", "GSM2330388", "GSM2330389", "GSM2330390", "GSM2330391", "GSM2330392", "GSM2330393", "GSM2330394", "GSM2330395", "GSM2330396", "GSM2330397", "GSM2330398", "GSM2330399", "GSM2330400", "GSM2330401", "GSM2330402", "GSM2330403", "GSM2330404", "GSM2330405", "GSM2330406", "GSM2330407", "GSM2330408", "GSM2330409", "GSM2330410", "GSM2330411", "GSM2330412", "GSM2330413", "GSM2330414", "GSM2330415", "GSM2330416", "GSM2330417", "GSM2330418", "GSM2330419", "GSM2330420", "GSM2330421", "GSM2330422", "GSM2330423", "GSM2330424", "GSM2330425", "GSM2330426", "GSM2330427", "GSM2330428", "GSM2330429", "GSM2330430", "GSM2330431", "GSM2330432", "GSM2330433", "GSM2330434", "GSM2330435", "GSM2330436", "GSM2330437", "GSM2330438", "GSM2330439", "GSM2330440", "GSM2330441", "GSM2330442", "GSM2330443", "GSM2330444", "GSM2330445", "GSM2330446", "GSM2330447", "GSM2330448", "GSM2330449", "GSM2330450", "GSM2330451", "GSM2330452", "GSM2330453", "GSM2330454", "GSM2330455", "GSM2330456", "GSM2330457", "GSM2330458", "GSM2330459", "GSM2330460", "GSM2330461", "GSM2330462", "GSM2330463", "GSM2330464", "GSM2330465", "GSM2330466", "GSM2330467", "GSM2330468", "GSM2330469", "GSM2330470", "GSM2330471", "GSM2330472", "GSM2330473", "GSM2330474", "GSM2330475", "GSM2330476", "GSM2330477", "GSM2330478", "GSM2330479", "GSM2330480", "GSM2330481", "GSM2330482", "GSM2330483", "GSM2330484", "GSM2330485", "GSM2330486", "GSM2330487", "GSM2330488", "GSM2330489", "GSM2330490", "GSM2330491", "GSM2330492", "GSM2330493", "GSM2330494", "GSM2330495", "GSM2330496", "GSM2330497", "GSM2330498", "GSM2330499", "GSM2330500", "GSM2330501", "GSM2330502", "GSM2330503", "GSM2330504", "GSM2330505", "GSM2330506", "GSM2330507", "GSM2330508", "GSM2330509", "GSM2330510", "GSM2330511", "GSM2330512", "GSM2330513", "GSM2330514"], "sample_count": 218, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Z1031B Paired Gene Expression", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31506496:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9dc76a766b1aec9cb6b37a9cf071a66e27dd7b4c7c0cb8fb4a1698a949967b43", "bytes": 886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "The comparison of test ligands (AIs) and native ligand of RAD51.", "structure": {"pmcid": "PMC6736845", "section_index": 11, "section_title": "RAD51 potentially bound to AIs", "row_count": 14, "column_count": 4}, "table": {"label": "Table 1", "caption": "The comparison of test ligands (AIs) and native ligand of RAD51.", "rows": [["Native Ligand", "Test Ligands"], ["Exemestane (60198)", "Anastrozole (2187)", "Letrozole (3902)"], ["LEU A 252", "LEU A 252", "—", "LEU A 252"], ["ARG A 250", "ARG A 250", "ARG A 250", "ARG A 250"], ["ARG A 247", "ARG A 247", "ARG A 247", "ARG A 247"], ["PHE A 248", "PHE A 248", "PHE A 248", "PHE A 248"], ["ARG A 254", "ARG A 254", "ARG A 254", "ARG A 254"], ["PHE B1546", "PHE B1546", "PHE B1546", "PHE B1546"], ["LEU A 255", "LEU A 255", "—", "LEU A 255"], ["LEU A 204", "LEU A 204", "LEU A 204", "LEU A 204"], ["TYR A 205", "TYR A 205", "TYR A 205", "—"], ["—", "TYR A 201", "THR A 201", "TYR A 201"], ["9", "10", "8", "9"], ["(Identical Residues: 9)", "(Identical Residues: 7)", "(Identical Residues: 8)"]], "row_count": 14, "column_count": 4, "numeric_cells": 46, "header_rows": 2, "locator": "section[11]/table-wrap[1]#Tab1"}}], "gaps": ["asset:data:geo:GSE87411 not downloaded", "asset:data:geo:GSE87411 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Wilcoxon rank-sum and Fisher exact tests were used to analyze the association between gene expression and clinical characteristics. Pearson correlation was applied to calculate different parameters in terms of correlation. T test was performed for the evaluation of differences between groups. The criteria of P value < 0.05 was determined to be significantly different."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "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"}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE87411"], "resolved_accessions": ["GSE87411"], "statements": ["All data is provided in the manuscript."], "basis": "The paper names GSE87411 in NCBI Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31506496", "data:geo:GSE87411", "asset:table:pmid:31506496:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE87411"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25367, "completion_tokens": 2004, "cached_tokens": 8448}}, "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:31506496", "type": "paper", "label": "pmid:31506496"}, {"id": "source:pmid:31506496", "type": "manuscript", "label": "PMID 31506496 full text"}, {"id": "data:geo:GSE87411", "type": "dataset", "label": "GEO GSE87411"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31506496", "type": "paper", "label": "pmid:31506496"}, {"id": "source:pmid:31506496", "type": "manuscript", "label": "PMID 31506496 full text"}, {"id": "data:geo:GSE87411", "type": "dataset", "label": "GEO GSE87411"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31506496", "type": "extraction", "used": ["source:pmid:31506496"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE87411", "type": "accession_resolution", "used": ["data:geo:GSE87411"], "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:31506496", "parent_hash": "sha256:9f2c1d9f44b0a2835646f9601d77fbc96ead9671d357447766a9b8d17e4e1888", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE87411 licence not read", "asset:data:geo:GSE87411 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ast cancer to neoadjuvant endocrine therapy. Microarray data of GSE87411 contained 109 pairs of samp"], "order_basis": "paper_text_order:475", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Wilcoxon rank-sum and Fisher exact tests were used to analyze the association between gene expression and clinical characteristics. Pearson correlation was applied to calculate different parameters in terms of correlation. T test was performed for the evaluation of differences between groups. The criteria of P value < 0.05 was determined to be significantly different."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}