Bioinformatics-based identification of miR-542-5p as a predictive biomarker in breast cancer therapy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29371858", "kind": "science-record", "revision": 8, "content_hash": "sha256:2e2b6645bb2d0c19ee6f09ddbca9779d39d4e7a6bd689bad97bd156baf924e0c", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T22:43:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based identification of miR-542-5p as a predictive biomarker in breast cancer therapy.", "doi": "10.1186/s41065-018-0055-7", "pmid": "29371858", "authors": ["Qiong-Ni Zhu", "Helen Renaud", "Ying Guo"], "journal": "Hereditas", "year": 2018, "abstract": "BACKGROUND: Tamoxifen is the first-line hormone therapy for estrogen receptor alpha positive (ERα+) breast cancer. However, about 40% of patients with ERα + breast cancer who receive tamoxifen therapy eventually develop resistance resulting in a poor prognosis. The aim of this study was to mine available data sets in the Gene Expression Omnibus (GEO) database, including in vitro (cell lines) and in vivo (tissue samples), and to identify all miRNAs associated with tamoxifen resistance (TamR) in breast cancer. Secondly, this study aimed to predict the key gene regulatory networks of newly found TamR-related miRNAs and evaluate the potential role of the miRNAs and targets as potential prognosis biomarkers for breast cancer patients.\nRESULT: Microarray data sets from two different studies were used from the GEO database: 1. GSE66607: miRNA of MCF-7 TamR cells; 2. GSE37405: TamR tissues. Differentially expressed microRNAs (miRNAs) were identified in both data sets and 5 differentially expressed miRNAs were found to overlap between the two data sets. Profiles of GSE37405 and data from the Kaplan-Meier Plotter Database (KMPD) along with Gene Expression Profiling Interactive Analysis (GEPIA) were used to reveal the relationship between these 5 miRNAs and overall survival. The results showed that has-miR-542-5p was the only miRNA associated with overall survival of ERα + breast cancer patients who received adjuvant tamoxifen. Targets of has-miR-542-5p were predicted by miRanda and TargetScan, and the mRNA expression of the three 3 target gene, Tyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Beta (YWHAB), Lymphocyte Antigen 9 (LY9), and Secreted Frizzled Related Protein 1 (SFRP1) were associated with overall survival in 2 different databases. Copy-number alterations (CNAs) of SFRP1 confer survival disadvantage to breast cancer patients and alter the mRNA expression of SFRP1 in cBioPortal database.\nCONCLUSION: This study indicates that miRNA has-miR-542-5p is associated with TamR and can predict prognosis of breast cancer patients. Furthermore, has-miR-542-5p may be acting through a mechanism involving the target genes YWHAB, LY9, and SFRP1. Overall, has-miR-542-5p is a predictive biomarker and potential target for therapy of breast cancer patients.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier overall survival curves were computed and compared using the log-rank statistic.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29371858", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Kaplan-Meier overall survival curves were computed and compared using the log-rank statistic."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data produced by the study are disclosed in the manuscript and the additional files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29371858", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "All data produced by the study are disclosed in the manuscript and the additional files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:29371858"], "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:GSE37405"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE37405"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29371858", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s41065-018-0055-7", "sha256": "sha256:0c2d318a0fa930cea26ac9ce7583719ca259f88a0dfaad8400edfa0d0115416c", "bytes": 41073, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s41065-018-0055-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5769523", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37405", "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=GSE37405", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37405", "version": null, "note": "All data produced by the study are disclosed in the manuscript and the additional files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data produced by the study are disclosed in the manuscript and the additional files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM917834", "GSM917835", "GSM917836", "GSM917837", "GSM917838", "GSM917839", "GSM917840", "GSM917841", "GSM917842", "GSM917843", "GSM917844", "GSM917845", "GSM917846", "GSM917847", "GSM917848", "GSM917849", "GSM917850", "GSM917851", "GSM917852", "GSM917853", "GSM917854", "GSM917855", "GSM917856", "GSM917857", "GSM917858", "GSM917859", "GSM917860", "GSM917861", "GSM917862", "GSM917863", "GSM917864", "GSM917865", "GSM917866", "GSM917867", "GSM917868", "GSM917869", "GSM917870", "GSM917871", "GSM917872", "GSM917873", "GSM917874", "GSM917875", "GSM917876", "GSM917877", "GSM917878", "GSM917879", "GSM917880", "GSM917881", "GSM917882", "GSM917883", "GSM917884", "GSM917885", "GSM917886", "GSM917887", "GSM917888", "GSM917889", "GSM917890", "GSM917891", "GSM917892", "GSM917893", "GSM917894", "GSM917895", "GSM917896", "GSM917897", "GSM917898", "GSM917899", "GSM917900", "GSM917901", "GSM917902", "GSM917903", "GSM917904", "GSM917905", "GSM917906", "GSM917907", "GSM917908", "GSM917909", "GSM917910", "GSM917911", "GSM917912", "GSM917913", "GSM917914", "GSM917915", "GSM917916", "GSM917917", "GSM917918", "GSM917919", "GSM917920", "GSM917921", "GSM917922", "GSM917923", "GSM917924", "GSM917925", "GSM917926", "GSM917927", "GSM917928", "GSM917929", "GSM917930", "GSM917931", "GSM917932", "GSM917933", "GSM917934", "GSM917935", "GSM917936", "GSM917937", "GSM917938", "GSM917939", "GSM917940", "GSM917941", "GSM917942", "GSM917943", "GSM917944", "GSM917945", "GSM917946", "GSM917971", "GSM917972", "GSM917973", "GSM917974", "GSM917975", "GSM917976", "GSM917977", "GSM917978", "GSM917979", "GSM917980", "GSM917981", "GSM917982", "GSM917983", "GSM917984", "GSM917985", "GSM917986", "GSM917987", "GSM917988", "GSM917989", "GSM917990", "GSM917991", "GSM917992", "GSM917993", "GSM917994", "GSM917995", "GSM917996", "GSM917997", "GSM917998", "GSM917999", "GSM918000", "GSM918001", "GSM918002", "GSM918003", "GSM918004", "GSM918005", "GSM918006", "GSM918007", "GSM918008", "GSM918009", "GSM918010"], "sample_count": 153, "group_sizes": null, "group_sizes_basis": null, "platform": "15462;14149;13703", "taxon": "Murid gammaherpesvirus 4; Betapolyomavirus hominis; Homo sapiens; Human alphaherpesvirus 1; Human betaherpesvirus 5; Murid betaherpesvirus 1; Human immunodeficiency virus 1; human gammaherpesvirus 4; JC polyomavirus; Human gammaherpesvirus 8; Betapolyomavirus macacae", "title": "Global microRNA expression profiling of high-risk ER+ breast cancers from patients receiving adjuvant Tamoxifen mono-therapy: a DBCG study", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE66607", "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=GSE66607", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66607", "version": null, "note": "All data produced by the study are disclosed in the manuscript and the additional files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data produced by the study are disclosed in the manuscript and the additional files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1626115", "GSM1626116"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "16384", "taxon": "synthetic construct; Homo sapiens", "title": "Identification of differently expressed miRNAs between Tamoxifen sensitive cells and Tamoxifen resistant cells", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE37405 not downloaded", "asset:data:geo:GSE37405 licence not read", "asset:data:geo:GSE66607 not downloaded", "asset:data:geo:GSE66607 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Kaplan-Meier overall survival curves were computed and compared using the log-rank statistic."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE66607", "GSE37405"], "resolved_accessions": ["GSE66607", "GSE37405"], "statements": ["All data produced by the study are disclosed in the manuscript and the additional files."], "basis": "The paper names GSE66607, GSE37405 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:29371858", "data:geo:GSE37405"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE37405"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:29371858", "type": "paper", "label": "pmid:29371858"}, {"id": "source:pmid:29371858", "type": "manuscript", "label": "PMID 29371858 full text"}, {"id": "data:geo:GSE37405", "type": "dataset", "label": "GEO GSE37405"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29371858", "type": "paper", "label": "pmid:29371858"}, {"id": "source:pmid:29371858", "type": "manuscript", "label": "PMID 29371858 full text"}, {"id": "data:geo:GSE37405", "type": "dataset", "label": "GEO GSE37405"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29371858", "type": "extraction", "used": ["source:pmid:29371858"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE37405", "type": "accession_resolution", "used": ["data:geo:GSE37405"], "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:29371858", "parent_hash": "sha256:4b9d48119731e3d909a3adfbffe0f58c0e8d03250c9f062833ad1cf4ff402d08", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE37405 licence not read", "asset:data:geo:GSE37405 not downloaded", "asset:data:geo:GSE66607 licence not read", "asset:data:geo:GSE66607 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["atabase, including in vitro (cell lines) and in vivo (tissue samples), and to identify all miRNAs"], "order_basis": "paper_text_order:456", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["omarkers for breast cancer patients. RESULT: Microarray data sets from two different studies were us", "Statistical analysis For each triplicate of microarray data, analysis of variance for comparisons b"], "order_basis": "paper_text_order:805", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["from the GEO database: 1. GSE66607: miRNA of MCF-7 TamR cells; 2. GSE37405: TamR tissues. Diffe"], "order_basis": "paper_text_order:908", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier overall survival curves were computed and compared using the log-rank statistic."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}