MiR-1-3p Suppresses Colorectal Cancer Cell Proliferation and Metastasis by Inhibiting YWHAZ-Mediated Epithelial-Mesenchymal Transition.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33718221", "kind": "science-record", "revision": 7, "content_hash": "sha256:0e4bf83db27ba8ac72411cccf4f4dad41b3df583c3ffa03945f5c2f8bf98e9bd", "created_at": "2026-11-01T15:41:28Z", "updated_at": "2026-11-01T22:03:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "MiR-1-3p Suppresses Colorectal Cancer Cell Proliferation and Metastasis by Inhibiting YWHAZ-Mediated Epithelial-Mesenchymal Transition.", "doi": "10.3389/fonc.2021.634596", "pmid": "33718221", "authors": ["Guanghong Du", "Xuelian Yu", "Yun Chen", "Wangting Cai"], "journal": "Frontiers in oncology", "year": 2021, "abstract": "BACKGROUND: Colorectal cancer (CRC) is regarded as one of the most common malignancies in the world. MiR-1-3p was reported to be a tumor suppressor in CRC. However, the mechanisms have not been fully elucidated.\nMETHODS: To identify CRC-associated miRNA, microarray data set GSE30454 was downloaded from the Gene Expression Omnibus database (GEO), and miR-1-3p was screened out as a candidate. The expression of miR-1-3p was detected using quantitative real-time polymerase chain reaction (qRT-PCR) in CRC cell lines and tissues. CCK-8 assay and transwell invasion assay were performed to determine CRC cell line proliferation and invasion, respectively. The levels of YWHAZ and EMT-associated proteins were detected using western blotting.\nRESULTS: Bioinformatic analysis showed that miR-1-3p was downregulated in CRC tissues, which is verified by our experimental validation. The overexpression of miR-1-3p significantly suppressed CRC cell proliferation and invasion. Further studies showed that YWHAZ was a direct target of miR-1-3p and mediated epithelial-mesenchymal transition (EMT) modulated by miR-1-3p.\nCONCLUSION: Our results demonstrated that miR-1-3p suppresses colorectal cancer cell proliferation and metastasis through regulating YWHAZ-mediated EMT, which may support a novel therapeutic strategy for CRC patients.", "claims": [{"id": "claim-method", "statement": "The correlation between miR-1-3p and YWHAZ was determined using the Spearman rank correlation test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33718221", "locator": "sections[12] \"Statistical Analysis\" paragraph 2", "quote": "The correlation between miR-1-3p and YWHAZ was determined using the Spearman rank correlation test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33718221", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."}], "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:33718221"], "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:GSE10259"], "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:GSE10259"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33718221", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2021.634596", "sha256": "sha256:34c411a6d324c54e1b871898d99d9e3c73d9805413f9ea115684503abfb76405", "bytes": 28045, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2021.634596", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7952857", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10259", "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=GSE10259", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10259", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM259102", "GSM259103", "GSM259104", "GSM259105", "GSM259106", "GSM259107", "GSM259108", "GSM259109", "GSM259110", "GSM259111", "GSM259112", "GSM259113", "GSM259114", "GSM259115", "GSM259116", "GSM259117", "GSM259118", "GSM259119", "GSM259120", "GSM259121", "GSM259122", "GSM259123", "GSM259124", "GSM259125", "GSM259126", "GSM259127", "GSM259128", "GSM259129", "GSM259130", "GSM259131", "GSM259132", "GSM259133", "GSM259134", "GSM259135", "GSM259136", "GSM259137", "GSM259138", "GSM259139", "GSM259140", "GSM259141", "GSM259142", "GSM259143", "GSM259144", "GSM259145", "GSM259146", "GSM259147", "GSM259148", "GSM259149", "GSM259150", "GSM259151", "GSM259152", "GSM259153", "GSM259154", "GSM259155", "GSM259156", "GSM259157", "GSM259158", "GSM259159", "GSM259160", "GSM259161", "GSM259162", "GSM259163", "GSM259164", "GSM259165", "GSM259166", "GSM259167"], "sample_count": 66, "group_sizes": null, "group_sizes_basis": null, "platform": "4411", "taxon": "Mus musculus; Rattus norvegicus; Homo sapiens", "title": "Characterization of microRNA expression in colorectal cancer", "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:GSE29760", "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=GSE29760", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29760", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM737632", "GSM737633"], "sample_count": 2, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Expression signature in a human colorectal cancer cell line HCT116 transfected with miR-1 precursor molecule", "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:GSE30454", "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=GSE30454", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30454", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM755304", "GSM755305", "GSM755306", "GSM755307", "GSM755308", "GSM755309", "GSM755310", "GSM755311", "GSM755312", "GSM755313", "GSM755314", "GSM755315", "GSM755316", "GSM755317", "GSM755318", "GSM755319", "GSM755320", "GSM755321", "GSM755322", "GSM755323", "GSM755324", "GSM755325", "GSM755326", "GSM755327", "GSM755328", "GSM755329", "GSM755330", "GSM755331", "GSM755332", "GSM755333", "GSM755334", "GSM755335", "GSM755336", "GSM755337", "GSM755338", "GSM755339", "GSM755340", "GSM755341", "GSM755342", "GSM755343", "GSM755344", "GSM755345", "GSM755346", "GSM755347", "GSM755348", "GSM755349", "GSM755350", "GSM755351", "GSM755352", "GSM755353", "GSM755354", "GSM755355", "GSM755356", "GSM755357", "GSM755358", "GSM755359", "GSM755360", "GSM755361", "GSM755362", "GSM755363", "GSM755364", "GSM755365", "GSM755366", "GSM755367", "GSM755368", "GSM755369", "GSM755370", "GSM755371", "GSM755372", "GSM755373", "GSM755374", "GSM755375", "GSM755376", "GSM755377"], "sample_count": 74, "group_sizes": null, "group_sizes_basis": null, "platform": "8179", "taxon": "Homo sapiens", "title": "Colorectal cancers with microsatellite instability display unique miRNA profiles", "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:GSE35982", "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=GSE35982", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35982", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM878566", "GSM878567", "GSM878568", "GSM878569", "GSM878570", "GSM878571", "GSM878572", "GSM878573", "GSM878574", "GSM878575", "GSM878576", "GSM878577", "GSM878578", "GSM878579", "GSM878580", "GSM878581", "GSM878680", "GSM878681", "GSM878682", "GSM878683", "GSM878684", "GSM878685", "GSM878686", "GSM878687", "GSM878688", "GSM878689", "GSM878690", "GSM878691", "GSM878692", "GSM878693", "GSM878694", "GSM878695"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "14767;4133", "taxon": "Homo sapiens", "title": "Identifying microRNA-mRNA regulatory networks in colorectal cancer by a combination of expression profile and bioinformatics analysis", "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:GSE38389", "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=GSE38389", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38389", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM941048", "GSM941049", "GSM941050", "GSM941051", "GSM941052", "GSM941053", "GSM941054", "GSM941055", "GSM941056", "GSM941057", "GSM941058", "GSM941059", "GSM941060", "GSM941061", "GSM941062", "GSM941063", "GSM941064", "GSM941065", "GSM941066", "GSM941067", "GSM941068", "GSM941069", "GSM941070", "GSM941071", "GSM941072", "GSM941073", "GSM941074", "GSM941075", "GSM941076", "GSM941077", "GSM941078", "GSM941079", "GSM941080", "GSM941081", "GSM941082", "GSM941083", "GSM941084", "GSM941085", "GSM941086", "GSM941087", "GSM941088", "GSM941089", "GSM941090", "GSM941091", "GSM941092", "GSM941093", "GSM941094", "GSM941095", "GSM941096", "GSM941097", "GSM941098", "GSM941099", "GSM941100", "GSM941101", "GSM941102", "GSM941103", "GSM941104", "GSM941105", "GSM941106", "GSM941107", "GSM941108", "GSM941109", "GSM941110", "GSM941111", "GSM941112", "GSM941113", "GSM941114", "GSM941115", "GSM941116", "GSM941117", "GSM941118", "GSM941119", "GSM941120", "GSM941121", "GSM941122", "GSM941123", "GSM941124", "GSM941125", "GSM941126", "GSM941127", "GSM941128", "GSM941129", "GSM941130", "GSM941131", "GSM941132", "GSM941133", "GSM941134", "GSM941135", "GSM941136", "GSM941137", "GSM941138", "GSM941139", "GSM941140", "GSM941141", "GSM941142", "GSM941143", "GSM941144", "GSM941145", "GSM941146", "GSM941147", "GSM941148", "GSM941149", "GSM941150", "GSM941151", "GSM941152", "GSM941153", "GSM941154", "GSM941155", "GSM941156", "GSM941157", "GSM941158", "GSM941159", "GSM941160", "GSM941161", "GSM941162", "GSM941163", "GSM941164", "GSM941165", "GSM941166", "GSM941167", "GSM941168", "GSM941169", "GSM941170", "GSM941171", "GSM941172", "GSM941173", "GSM941174", "GSM941175", "GSM941176", "GSM941177", "GSM941178", "GSM941179", "GSM941180", "GSM941181", "GSM941182", "GSM941183", "GSM941184", "GSM941185", "GSM941186", "GSM941187"], "sample_count": 140, "group_sizes": null, "group_sizes_basis": null, "platform": "11039", "taxon": "Homo sapiens", "title": "The rectal cancer microRNAome - a comprehensive comparative analysis of microRNA expression in rectal cancer and matched normal mucosa", "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:GSE41655", "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=GSE41655", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41655", "version": null, "note": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1021014", "GSM1021015", "GSM1021016", "GSM1021017", "GSM1021018", "GSM1021019", "GSM1021020", "GSM1021021", "GSM1021022", "GSM1021023", "GSM1021024", "GSM1021025", "GSM1021026", "GSM1021027", "GSM1021028", "GSM1021029", "GSM1021030", "GSM1021031", "GSM1021032", "GSM1021033", "GSM1021034", "GSM1021035", "GSM1021036", "GSM1021037", "GSM1021038", "GSM1021039", "GSM1021040", "GSM1021041", "GSM1021042", "GSM1021043", "GSM1021044", "GSM1021045", "GSM1021046", "GSM1021047", "GSM1021048", "GSM1021049", "GSM1021050", "GSM1021051", "GSM1021052", "GSM1021053", "GSM1021054", "GSM1021055", "GSM1021056", "GSM1021057", "GSM1021058", "GSM1021059", "GSM1021060", "GSM1021061", "GSM1021062", "GSM1021063", "GSM1021064", "GSM1021065", "GSM1021066", "GSM1021067", "GSM1021068", "GSM1021069", "GSM1021070", "GSM1021071", "GSM1021072", "GSM1021073", "GSM1021074", "GSM1021075", "GSM1021076", "GSM1021077", "GSM1021078", "GSM1021079", "GSM1021080", "GSM1021081", "GSM1021082", "GSM1021083", "GSM1021084", "GSM1021085", "GSM1021086", "GSM1021087", "GSM1021088", "GSM1021089", "GSM1021090", "GSM1021091", "GSM1021092", "GSM1021093", "GSM1021094", "GSM1021095", "GSM1021096", "GSM1021097", "GSM1021098", "GSM1021099", "GSM1021100", "GSM1021101", "GSM1021102", "GSM1021103", "GSM1021104", "GSM1021105", "GSM1021106", "GSM1021107", "GSM1021108", "GSM1021109", "GSM1021110", "GSM1021111", "GSM1021112", "GSM1021113", "GSM1021114", "GSM1021115", "GSM1021116", "GSM1021117", "GSM1021118", "GSM1021119", "GSM1021120"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "11487", "taxon": "Homo sapiens", "title": "MicroRNA expression profiling of colorectal normal mucosa, adenoma and adenocarcinoma tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33718221:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:304ac38e3e66986a3133e6109b76ccd539e38c44a5d5e6c57f5fb569e9262789", "bytes": 1095, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "Top 10 DEMs between CRC tissues and normal colonic mucosa samples from the miRNA profiling GSE30454.", "structure": {"pmcid": "PMC7952857", "section_index": 14, "section_title": "MiR-1-3p Was Downregulated in CRC Tissues and Cell Lines", "row_count": 13, "column_count": 6}, "table": {"label": "Table 1", "caption": "Top 10 DEMs between CRC tissues and normal colonic mucosa samples from the miRNA profiling GSE30454.", "rows": [["miRNA", "logFC", "t", "B", "P.Value", "adj.P.Val"], ["Down-regulated", "", "", "", "", ""], ["hsa-miR-129-5p", "−2.77804", "−10.55171", "20.4586", "2.03E-13", "5.81E-11"], ["hsa-miR-1-3p", "−2.74918", "−9.63754", "17.7827", "3.11E-12", "5.09E-10"], ["hsa-miR-137-3p", "−2.27167", "−11.9235", "24.2607", "4.12E-15", "4.72E-12"], ["hsa-miR-488-3p", "−1.82694", "−10.89459", "21.4332", "7.49E-14", "2.86E-11"], ["hsa-miR-153-3p", "−1.34732", "−10.0189", "18.9125", "9.84E-13", "2.25E-10"], ["Up-regulated", "", "", "", "", ""], ["hsa-miR-1273a", "3.53691", "6.62772", "8.3016", "4.82E-08", "1.31E-06"], ["hsa-miR-31-5p", "2.86879", "7.72831", "11.8621", "1.29E-09", "5.67E-08"], ["hsa-miR-663b", "1.46511", "7.08333", "9.7834", "1.07E-08", "3.94E-07"], ["hsa-miR-183-5p", "1.96749", "11.03949", "21.8401", "4.94E-14", "2.83E-11"], ["hsa-miR-1826", "1.27283", "9.7969", "18.2571", "1.92E-12", "3.66E-10"]], "row_count": 13, "column_count": 6, "numeric_cells": 60, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T1"}}], "gaps": ["asset:data:geo:GSE10259 not downloaded", "asset:data:geo:GSE10259 licence not read", "asset:data:geo:GSE29760 not downloaded", "asset:data:geo:GSE29760 licence not read", "asset:data:geo:GSE30454 not downloaded", "asset:data:geo:GSE30454 licence not read", "asset:data:geo:GSE35982 not downloaded", "asset:data:geo:GSE35982 licence not read", "asset:data:geo:GSE38389 not downloaded", "asset:data:geo:GSE38389 licence not read", "asset:data:geo:GSE41655 not downloaded", "asset:data:geo:GSE41655 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The correlation between miR-1-3p and YWHAZ was determined using the Spearman rank correlation test."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Student t-test"}}, {"id": "method-3", "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": ["spearman_rho"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: spearman."}, "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": ["GSE30454", "GSE38389", "GSE10259", "GSE41655", "GSE35982", "GSE29760"], "resolved_accessions": ["GSE30454", "GSE38389", "GSE10259", "GSE41655", "GSE35982", "GSE29760"], "statements": ["The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation."], "basis": "The paper names GSE30454, GSE38389, GSE10259, GSE41655, GSE35982, GSE29760 in Gene Expression Omnibus database (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["spearman_rho"], "assets": ["source:pmid:33718221", "data:geo:GSE10259", "asset:table:pmid:33718221:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10259"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:56Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25706, "completion_tokens": 2207, "cached_tokens": 8712}}, "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:33718221", "type": "paper", "label": "pmid:33718221"}, {"id": "source:pmid:33718221", "type": "manuscript", "label": "PMID 33718221 full text"}, {"id": "data:geo:GSE10259", "type": "dataset", "label": "GEO GSE10259"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33718221", "type": "paper", "label": "pmid:33718221"}, {"id": "source:pmid:33718221", "type": "manuscript", "label": "PMID 33718221 full text"}, {"id": "data:geo:GSE10259", "type": "dataset", "label": "GEO GSE10259"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33718221", "type": "extraction", "used": ["source:pmid:33718221"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10259", "type": "accession_resolution", "used": ["data:geo:GSE10259"], "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:33718221", "parent_hash": "sha256:7f1cebd858358b972b1037811970ba60193bc0836c8cb4268bc9bd689edc634e", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE10259 licence not read", "asset:data:geo:GSE10259 not downloaded", "asset:data:geo:GSE29760 licence not read", "asset:data:geo:GSE29760 not downloaded", "asset:data:geo:GSE30454 licence not read", "asset:data:geo:GSE30454 not downloaded", "asset:data:geo:GSE35982 licence not read", "asset:data:geo:GSE35982 not downloaded", "asset:data:geo:GSE38389 licence not read", "asset:data:geo:GSE38389 not downloaded", "asset:data:geo:GSE41655 licence not read", "asset:data:geo:GSE41655 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": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": [". METHODS: To identify CRC-associated miRNA, microarray data set GSE30454 was downloaded from the Ge"], "order_basis": "paper_text_order:346", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ion (qRT-PCR) in CRC cell lines and tissues. CCK-8 assay and transwell invasion assay were perf", "ANOVA test were carried out for qRT-PCR and CCK-8 analyses. The correlation between miR-1-3p a"], "order_basis": "paper_text_order:621", "id": "assay:2"}, {"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": ["EMT-associated proteins were detected using western blotting. RESULTS: Bioinformatic analysis showed that"], "order_basis": "paper_text_order:815", "id": "assay:3"}, {"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": ["nsents were obtained. Cell Culture and miRNA Transfection Human CRC cell lines (HT29, HCT116, SW480) w", "at 37°C. MiRNAs and expression plasmids were transfected into cells by Lipofectamine 2000 reagent (In"], "order_basis": "paper_text_order:1867", "id": "assay:4"}, {"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": ["American Type Culture Collection, ATCC) were cultured in RPMI 1640 (Hyclone) supplemented with 10% fe"], "order_basis": "paper_text_order:2008", "id": "assay:5"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The correlation between miR-1-3p and YWHAZ was determined using the Spearman rank correlation test."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}