← All .science files
pmid:26020378
Downregulated miR-495 [Corrected] Inhibits the G1-S Phase Transition by Targeting Bmi-1 in Breast Cancer.
Lan Wang · Jun-Ling Liu · Liang Yu · Xiang-Xia Liu · Hong-Mei Wu · Fang-Yong Lei · Shu Wu · Xi Wang
Medicine · 2015 doi:10.1097/MD.0000000000000718
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 · 8 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] 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 · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 116 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
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 · 2 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 · 0 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 · 7 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[4] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[5] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[6] 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:26020378", "kind": "science-record", "revision": 7, "content_hash": "sha256:4a30338f5cfe18e3f896b4e6f06202d18f6aa3220687f33cca893897341f08f1", "created_at": "2026-11-01T15:40:08Z", "updated_at": "2026-11-01T21:58:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Downregulated miR-495 [Corrected] Inhibits the G1-S Phase Transition by Targeting Bmi-1 in Breast Cancer.", "doi": "10.1097/MD.0000000000000718", "pmid": "26020378", "authors": ["Lan Wang", "Jun-Ling Liu", "Liang Yu", "Xiang-Xia Liu", "Hong-Mei Wu", "Fang-Yong Lei", "Shu Wu", "Xi Wang"], "journal": "Medicine", "year": 2015, "abstract": "Bmi-1 (B cell-specific Moloney murine leukemia virus integration site 1) is upregulated in breast cancer and was involved in many malignant progressions of breast cells, including cell proliferation, stem cell pluripotency, and cancer initiation. However, the epigenetic regulatory mechanism of Bmi-1 in breast cancer remains unclear. After analysis of the ArrayExpress dataset GSE45666, we comparatively detected the expression levels of miR-495 in 9 examined breast cancer cell lines, normal breast epithelial cells and 8 pairs of fresh clinical tumor samples. Furthermore, to evaluate the effect of miR-495 on the progression of breast cancer, MCF-7 and MDA-MB-231 were transduced to stably overexpress miR-495. The 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay, colony formation assays, 5-Bromo-2-deoxyUridine labeling and immunofluorescence, anchorage-independent growth ability assay, flow cytometry analysis, and luciferase assays were used to test the effect of miR-495 in MCF-7 and MDA-MB-231 cells in vitro. Xenografted tumor model was also used to evaluate the effect of miR-495 in breast cancer. Herein, we found that miR-495, a predicted regulator of Bmi-1, was frequently downregulated in malignant cells and tissues of breast. Upregulation of miR-495 significantly suppressed breast cancer cell proliferation and tumorigenicity via G1-S arrest. Further analysis revealed that miR-495 targeted Bmi-1 through its 3' untranslated region. Moreover, Bmi-1 could neutralize the suppressive effect of miR-495 on cell proliferation and tumorigenicity of breast cancer in vivo. These data suggested that miR-495 could inhibit the G1-S phase transition that leads to proliferation and tumorigenicity inhibition by targeting and suppressing Bmi-1 in breast cancer.", "claims": [{"id": "claim-method", "statement": "Student t test in SPSS13.0 (IBM, Armonk, NY) was used to evaluate the significant difference of 2 groups of data in all the pertinent experiments. A P value <0.05 (using a 2-tailed paired t test) was considered statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26020378", "locator": "sections[14] \"Statistical Analysis\" paragraph 2", "quote": "Student t test in SPSS13.0 (IBM, Armonk, NY) was used to evaluate the significant difference of 2 groups of data in all the pertinent experiments. A P value <0.05 (using a 2-tailed paired t test) was considered statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (www.md-journal.com).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26020378", "locator": "sections[26] \"fn-group\" paragraph 1", "quote": "Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (www.md-journal.com)."}], "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:26020378"], "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:GSE45666"], "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:student_t", "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:GSE45666"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26020378", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000000718", "sha256": "sha256:16495d9e39d903a4386d133fb47826213a2291aa2c8c8d0102c5b4b1ef22cb58", "bytes": 32468, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000000718", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4616407", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE45666", "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=GSE45666", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45666", "version": null, "note": "Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (www.md-journal.com).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (www.md-journal.com).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1111512", "GSM1111513", "GSM1111514", "GSM1111515", "GSM1111516", "GSM1111517", "GSM1111518", "GSM1111519", "GSM1111520", "GSM1111521", "GSM1111522", "GSM1111523", "GSM1111524", "GSM1111525", "GSM1111526", "GSM1111527", "GSM1111528", "GSM1111529", "GSM1111530", "GSM1111531", "GSM1111532", "GSM1111533", "GSM1111534", "GSM1111535", "GSM1111536", "GSM1111537", "GSM1111538", "GSM1111539", "GSM1111540", "GSM1111541", "GSM1111542", "GSM1111543", "GSM1111544", "GSM1111545", "GSM1111546", "GSM1111547", "GSM1111548", "GSM1111549", "GSM1111550", "GSM1111551", "GSM1111552", "GSM1111553", "GSM1111554", "GSM1111555", "GSM1111556", "GSM1111557", "GSM1111558", "GSM1111559", "GSM1111560", "GSM1111561", "GSM1111562", "GSM1111563", "GSM1111564", "GSM1111565", "GSM1111566", "GSM1111567", "GSM1111568", "GSM1111569", "GSM1111570", "GSM1111571", "GSM1111572", "GSM1111573", "GSM1111574", "GSM1111575", "GSM1111576", "GSM1111577", "GSM1111578", "GSM1111579", "GSM1111580", "GSM1111581", "GSM1111582", "GSM1111583", "GSM1111584", "GSM1111585", "GSM1111586", "GSM1111587", "GSM1111588", "GSM1111589", "GSM1111590", "GSM1111591", "GSM1111592", "GSM1111593", "GSM1111594", "GSM1111595", "GSM1111596", "GSM1111597", "GSM1111598", "GSM1111599", "GSM1111600", "GSM1111601", "GSM1111602", "GSM1111603", "GSM1111604", "GSM1111605", "GSM1111606", "GSM1111607", "GSM1111608", "GSM1111609", "GSM1111610", "GSM1111611", "GSM1111612", "GSM1111613", "GSM1111614", "GSM1111615", "GSM1111616", "GSM1111617", "GSM1111618", "GSM1111619", "GSM1111620", "GSM1111621", "GSM1111622", "GSM1111623", "GSM1111624", "GSM1111625", "GSM1111626", "GSM1111627"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "14767", "taxon": "Homo sapiens", "title": "MicroRNA expression profile of breast cancer patients with adjacent normal control group.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE45666 not downloaded", "asset:data:geo:GSE45666 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student t test in SPSS13.0 (IBM, Armonk, NY) was used to evaluate the significant difference of 2 groups of data in all the pertinent experiments. A P value <0.05 (using a 2-tailed paired t test) was considered statistically significant."}}], "targets": [], "gaps": ["method.student_t"]}, "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": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE45666"], "resolved_accessions": ["GSE45666"], "statements": ["Supplemental digital content is available for this article. Direct URL citations appear in the printed text and are provided in the HTML and PDF versions of this article on the journal's Website (www.md-journal.com)."], "basis": "The paper names GSE45666 in ArrayExpress and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26020378", "data:geo:GSE45666"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE45666"]}, "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:26020378", "type": "paper", "label": "pmid:26020378"}, {"id": "source:pmid:26020378", "type": "manuscript", "label": "PMID 26020378 full text"}, {"id": "data:geo:GSE45666", "type": "dataset", "label": "GEO GSE45666"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26020378", "type": "paper", "label": "pmid:26020378"}, {"id": "source:pmid:26020378", "type": "manuscript", "label": "PMID 26020378 full text"}, {"id": "data:geo:GSE45666", "type": "dataset", "label": "GEO GSE45666"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26020378", "type": "extraction", "used": ["source:pmid:26020378"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE45666", "type": "accession_resolution", "used": ["data:geo:GSE45666"], "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:26020378", "parent_hash": "sha256:6609a3b6f1ff5aeaad6aebde6ff35e96106839191ae2c7bbefed8d4a16bcbc28", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE45666 licence not read", "asset:data:geo:GSE45666 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": 0.99, "evidence": ["Bmi-1 (B cell-specific Moloney murine leukemia virus integration site 1) is upregu", "feration and tumorigenicity of breast cancer in vivo. These data suggested that miR-495 could inh"], "order_basis": "paper_text_order:106", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["miR-495 on the progression of breast cancer, MCF-7 and MDA-MB-231 were transduced to stably ove", "s were used to test the effect of miR-495 in MCF-7 and MDA-MB-231 cells in vitro. Xenografted t"], "order_basis": "paper_text_order:708", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["assays, 5-Bromo-2-deoxyUridine labeling and immunofluorescence, anchorage-independent growth ability assay,"], "order_basis": "paper_text_order:915", "id": "assay:3"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["anchorage-independent growth ability assay, flow cytometry analysis, and luciferase assays were used to"], "order_basis": "paper_text_order:979", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["NBECs), breast cancer cell lines, and stably transfected cells were maintained according to our previ"], "order_basis": "paper_text_order:1954", "id": "assay:5"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["the expression of indicated genes tested by real-time PCR (red represents higher expression; green rep", "green represents lower expression tested by real-time PCR. (B) Correlation analysis between miR-495 an"], "order_basis": "paper_text_order:2761", "id": "assay:6"}, {"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": ["Student t test in SPSS13.0 (IBM, Armonk, NY) was used to evaluate the significant difference of 2 groups of data in all the pertinent experiments. A P value <0.05 (using a 2-tailed paired t test) was considered statistically significant."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}