← All .science files
pmid:34798882
MiR-149-3p promotes the cisplatin resistance and EMT in ovarian cancer through downregulating TIMP2 and CDKN1A.
Jin Wang · Lingxia Liu
Journal of ovarian research · 2021 doi:10.1186/s13048-021-00919-5
Paper
complete
Experiment
complete
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 · 2 items
claims array · 3 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[1] object · 6 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 · 0 items
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 · 25 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 34 items
gaps array · 4 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
evidence object · 3 fields
[1] object · 10 fields
dsl_operations array · 4 items
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 · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
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 · 9 items
assays array · 6 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
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[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 · 1 item
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:34798882", "kind": "science-record", "revision": 4, "content_hash": "sha256:030a84b60951386a8e82c0eb2ce2add5e22243e16ad28ac5e23a1a521c482420", "created_at": "2026-11-01T17:36:30Z", "updated_at": "2026-11-01T22:05:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MiR-149-3p promotes the cisplatin resistance and EMT in ovarian cancer through downregulating TIMP2 and CDKN1A.", "doi": "10.1186/s13048-021-00919-5", "pmid": "34798882", "authors": ["Jin Wang", "Lingxia Liu"], "journal": "Journal of ovarian research", "year": 2021, "abstract": "BACKGROUND: Ovarian cancer (OC), a kind of gynecological cancer, is characterized by high mortality rate, with microRNAs (miRNAs) playing essential roles in it. However, the clinical significance of miRNAs and their molecular mechanisms in OC are mostly unknown.\nMETHODS: miR-149-3p expression was predicted through Gene Expression Omnibus (GEO) data in OC and confirmed by q-PCR in various OC cells and tissues from patients with different clinical characteristics. Moreover, its roles in terms of proliferation, migration and invasion were measured by CCK-8, colony formation, wound healing and transwell assays in OC cells including cisplatin-resistant and cisplatin-sensitive cells. And its effect on epithelial-mesenchymal transition was also assessed through detecting related protein expression. Additionally, its potential targets were verified by dual luciferase assay and Ago-RIP assay. Finally, its oncogenic functions were explored in vivo.\nRESULTS: In data from GSE79943, GSE131790, and TCGA, miR-149-3p was found to be highly expressed in OC tissues and associated with poor survival. In metastasis and chemoresistant tissues and cisplatin-resistant OC cells, its high expression was confirmed. In terms of tumorigenic effects, miR-149-3p knockdown in cisplatin-resistant OC cells inhibited its cisplatin resistance and other malignant phenotypes, while miR-149-3p overexpression in cisplatin-resistant OC cells led to contrary results. Mechanistically, miR-149-3p targeted 3'UTR of CDKN1A and TIMP2 to function as an oncogenic miRNA.\nCONCLUSION: In brief, miR-149-3p promoted cisplatin resistance and EMT in OC by downregulating CDKN1A and TIMP2, which might provide a potential therapeutic target for OC treatment.", "claims": [{"id": "claim-method", "statement": "The data of patients with high miR-149-3p expression and low miR-149-3p expression was gathered from the Cancer Genome Atlas (TCGA), and survival probability was assessed by Kaplan Meier which was commonly used to evaluate the influences of various genes on survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34798882", "locator": "sections[6] \"Prognostic analysis\" paragraph 2", "quote": "The data of patients with high miR-149-3p expression and low miR-149-3p expression was gathered from the Cancer Genome Atlas (TCGA), and survival probability was assessed by Kaplan Meier which was commonly used to evaluate the influences of various genes on survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34798882", "locator": "sections[31] \"Availability of data and materials\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "High expression of miR-149-3p was correlated with poor overall survival, disease specific survival and progress free interval (Fig. 1E).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34798882", "locator": "sections[19] \"miR-149-3p is upregulated in OC and associated with poor clinical outcome\" paragraph 2", "quote": "High expression of miR-149-3p was correlated with poor overall survival, disease specific survival and progress free interval (Fig. 1E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "High expression of miR-149-3p was correlated with poor overall survival, disease specific survival and progress free interval (Fig. 1E).", "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:34798882"], "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:GSE131790"], "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:GSE131790"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34798882", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13048-021-00919-5", "sha256": "sha256:3be17194d77e1f6a764641fa4655affabcb82b1d9b1152e4916b4d5a6cf5c1a2", "bytes": 36653, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13048-021-00919-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8605569", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE131790", "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=GSE131790", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE131790", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3819808", "GSM3819809", "GSM3819810", "GSM3819811", "GSM3819812", "GSM3819813", "GSM3819814", "GSM3819815", "GSM3819816", "GSM3819817", "GSM3819818", "GSM3819819", "GSM3819820", "GSM3819821", "GSM3819822", "GSM3819823", "GSM3819824", "GSM3819825", "GSM3819826", "GSM3819827", "GSM3819828", "GSM3819829", "GSM3819830", "GSM3819831", "GSM3819832"], "sample_count": 25, "group_sizes": null, "group_sizes_basis": null, "platform": "8786", "taxon": "synthetic construct; Homo sapiens", "title": "MiRNA profiles of high grade serous papillary ovarian cancer tumors and normal fallopian tube epithelium", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE79943", "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=GSE79943", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79943", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2108823", "GSM2108824", "GSM2108825", "GSM2108826", "GSM2108827", "GSM2108828", "GSM2108829", "GSM2108830", "GSM2108831", "GSM2108832", "GSM2108833", "GSM2108834", "GSM2108835", "GSM2108836", "GSM2108837", "GSM2108838", "GSM2108839", "GSM2108840", "GSM2108841", "GSM2108842", "GSM2108843", "GSM2108844", "GSM2108845", "GSM2108846", "GSM2108847", "GSM2108848", "GSM2108849", "GSM2108850", "GSM2108851", "GSM2108852", "GSM2108853", "GSM2108854", "GSM2108855", "GSM2108856"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "16770", "taxon": "Homo sapiens", "title": "Serum microRNA analysis of primary ovarian cancer patients", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE131790 not downloaded", "asset:data:geo:GSE131790 licence not read", "asset:data:geo:GSE79943 not downloaded", "asset:data:geo:GSE79943 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": "The data of patients with high miR-149-3p expression and low miR-149-3p expression was gathered from the Cancer Genome Atlas (TCGA), and survival probability was assessed by Kaplan Meier which was commonly used to evaluate the influences of various genes on survival."}}, {"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": "ANOVA"}}], "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": ["GSE79943", "GSE131790"], "resolved_accessions": ["GSE79943", "GSE131790"], "statements": ["The data used to support the findings of this study are available from the corresponding author upon request."], "basis": "The paper names GSE79943, GSE131790 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:34798882", "data:geo:GSE131790"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE131790"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:08:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12237, "completion_tokens": 1465, "cached_tokens": 264}}, "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:34798882", "type": "paper", "label": "pmid:34798882"}, {"id": "source:pmid:34798882", "type": "manuscript", "label": "PMID 34798882 full text"}, {"id": "data:geo:GSE131790", "type": "dataset", "label": "GEO GSE131790"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34798882", "type": "paper", "label": "pmid:34798882"}, {"id": "source:pmid:34798882", "type": "manuscript", "label": "PMID 34798882 full text"}, {"id": "data:geo:GSE131790", "type": "dataset", "label": "GEO GSE131790"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34798882", "type": "extraction", "used": ["source:pmid:34798882"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE131790", "type": "accession_resolution", "used": ["data:geo:GSE131790"], "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:34798882", "parent_hash": "sha256:e3b009646100db76f652894c32ac65128087547b3d181cfdcfbd679d21620c65", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE131790 licence not read", "asset:data:geo:GSE131790 not downloaded", "asset:data:geo:GSE79943 licence not read", "asset:data:geo:GSE79943 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": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ion, migration and invasion were measured by CCK-8, colony formation, wound healing and transwe"], "order_basis": "paper_text_order:621", "id": "assay:1"}, {"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": ["nally, its oncogenic functions were explored in vivo. RESULTS: In data from GSE79943, GSE131790,"], "order_basis": "paper_text_order:1011", "id": "assay:2"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["In terms of tumorigenic effects, miR-149-3p knockdown in cisplatin-resistant OC cells inhibited it", "file 2: Supplementary Table 1. Sequences of siRNA and shRNA Against Specific Targets. Suppleme", "upplementary Table 1. Sequences of siRNA and shRNA Against Specific Targets. Supplementary Tabl"], "order_basis": "paper_text_order:1321", "id": "assay:3"}, {"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": ["Academy of Sciences (Shanghai, China). These cell lines were cultured in DMEM (Dulbecco’s modified Eagle’s medium)", "ces (Shanghai, China). These cell lines were cultured in DMEM (Dulbecco’s modified Eagle’s medium) su"], "order_basis": "paper_text_order:2657", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["error of the mean (SEM). The photographs of Western blot were analysed by Image J software. P < 0.05"], "order_basis": "paper_text_order:3092", "id": "assay:5"}, {"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": ["The data of patients with high miR-149-3p expression and low miR-149-3p expression was gathered from the Cancer Genome Atlas (TCGA), and survival probability was assessed by Kaplan Meier which was commonly used to evaluate the influences of various genes on survival."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}