Computational analysis of mRNA expression profiles identifies microRNA-29a/c as predictor of colorectal cancer early recurrence.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:22348113", "kind": "science-record", "revision": 7, "content_hash": "sha256:bd4950d8a53408a8aef196673175ab826cd3001045dfef3469271e655c95363e", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T21:19:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Computational analysis of mRNA expression profiles identifies microRNA-29a/c as predictor of colorectal cancer early recurrence.", "doi": "10.1371/journal.pone.0031587", "pmid": "22348113", "authors": ["Tai-Yue Kuo", "Edward Hsi", "I-Ping Yang", "Pei-Chien Tsai", "Jaw-Yuan Wang", "Suh-Hang Hank Juo"], "journal": "PloS one", "year": 2012, "abstract": "Colorectal cancer (CRC) is one of the leading malignant cancers with a rapid increase in incidence and mortality. The recurrences of CRC after curative resection are sometimes unavoidable and often take place within the first year after surgery. MicroRNAs may serve as biomarkers to predict early recurrence of CRC, but identifying them from over 1,400 known human microRNAs is challenging and costly. An alternative approach is to analyze existing expression data of messenger RNAs (mRNAs) because generally speaking the expression levels of microRNAs and their target mRNAs are inversely correlated. In this study, we extracted six mRNA expression data of CRC in four studies (GSE12032, GSE17538, GSE4526 and GSE17181) from the gene expression omnibus (GEO). We inferred microRNA expression profiles and performed computational analysis to identify microRNAs associated with CRC recurrence using the IMRE method based on the MicroCosm database that includes 568,071 microRNA-target connections between 711 microRNAs and 20,884 gene targets. Two microRNAs, miR-29a and miR-29c, were disclosed and further meta-analysis of the six mRNA expression datasets showed that these two microRNAs were highly significant based on the Fisher p-value combination (p = 9.14 × 10(-9) for miR-29a and p = 1.14 × 10(-6) for miR-29c). Furthermore, these two microRNAs were experimentally tested in 78 human CRC samples to validate their effect on early recurrence. Our empirical results showed that the two microRNAs were significantly down-regulated (p = 0.007 for miR-29a and p = 0.007 for miR-29c) in the early-recurrence patients. This study shows the feasibility of using mRNA profiles to indicate microRNAs. We also shows miR-29a/c could be potential biomarkers for CRC early recurrence.", "claims": [{"id": "claim-method", "statement": "The random effect model showed an effect size of 213.36 (95% CI: 147.38–279.34) for miR-29a and an effect size of 176.91 (95% CI: 111.63–242.18) for miR-29c.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22348113", "locator": "sections[11] \"Meta-analysis for miR-29a and miR-29c\" paragraph 2", "quote": "The random effect model showed an effect size of 213.36 (95% CI: 147.38–279.34) for miR-29a and an effect size of 176.91 (95% CI: 111.63–242.18) for miR-29c."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded their normalized mRNA expression data and sample information from the GEO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:22348113", "locator": "sections[3] \"Search strategy for mRNA datasets from GEO\" paragraph 2", "quote": "We downloaded their normalized mRNA expression data and sample information from the GEO."}], "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:22348113"], "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:GSE12032"], "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:GSE12032"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:22348113", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0031587", "sha256": "sha256:1a0dbb42f63d433638b3276fe8c4cfafd45f4e5a8ada7658f1123706b6e5bc80", "bytes": 36177, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0031587", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3278467", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE12032", "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=GSE12032", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12032", "version": null, "note": "We downloaded their normalized mRNA expression data and sample information from the GEO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded their normalized mRNA expression data and sample information from the GEO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM304101", "GSM304102", "GSM304103", "GSM304104", "GSM304105", "GSM304106", "GSM304107", "GSM304108", "GSM304109", "GSM304110", "GSM304111", "GSM304112", "GSM304113", "GSM304114", "GSM304115", "GSM304116", "GSM304117", "GSM304118", "GSM304119", "GSM304120", "GSM304121", "GSM304122", "GSM304123", "GSM304124", "GSM304125", "GSM304126", "GSM304127", "GSM304128", "GSM304129", "GSM304130", "GSM304131", "GSM304132", "GSM304133", "GSM304134", "GSM304135", "GSM304136", "GSM304137", "GSM304138", "GSM304139", "GSM304140", "GSM304141", "GSM304142", "GSM304143", "GSM304144", "GSM304145", "GSM304146", "GSM304147", "GSM304148", "GSM304149", "GSM304150", "GSM304151", "GSM304152", "GSM304153", "GSM304154", "GSM304155", "GSM304156", "GSM304157", "GSM304158", "GSM304159", "GSM304160", "GSM304161", "GSM304162", "GSM304163", "GSM304164", "GSM304165", "GSM304166", "GSM304167", "GSM304168", "GSM304169", "GSM304170", "GSM304171", "GSM304172", "GSM304173", "GSM304174", "GSM304175", "GSM304176", "GSM304177", "GSM304178", "GSM304179", "GSM304180", "GSM304181", "GSM304182", "GSM304183", "GSM304184", "GSM304185", "GSM304186", "GSM304187", "GSM304188", "GSM304189", "GSM304190", "GSM304191", "GSM304192", "GSM304193", "GSM304194", "GSM304195", "GSM304196", "GSM304197", "GSM304198", "GSM304199", "GSM304200", "GSM304201", "GSM304202", "GSM304203", "GSM304204", "GSM304205", "GSM304206", "GSM304207", "GSM304208", "GSM304209", "GSM304210", "GSM304211", "GSM304212", "GSM304213", "GSM304214", "GSM304215", "GSM304216", "GSM304217", "GSM304218", "GSM304219", "GSM304220", "GSM304221", "GSM304222", "GSM304223", "GSM304224", "GSM304225", "GSM304226", "GSM304227", "GSM304228", "GSM304229", "GSM304230", "GSM304231", "GSM304232", "GSM304233", "GSM304234", "GSM304235", "GSM304236", "GSM304237", "GSM304238", "GSM304239", "GSM304240", "GSM304241", "GSM304242", "GSM304243", "GSM304244", "GSM304245", "GSM304246", "GSM304247", "GSM304248", "GSM304249", "GSM304250", "GSM304251", "GSM304252", "GSM304253", "GSM304254", "GSM304255", "GSM304256", "GSM304257", "GSM304258", "GSM304259", "GSM467732", "GSM467733", "GSM467734", "GSM467735", "GSM467736", "GSM467737", "GSM467738", "GSM467739", "GSM467740", "GSM467741", "GSM467742", "GSM467743", "GSM467744", "GSM467745", "GSM467746", "GSM467747", "GSM467748", "GSM467749", "GSM467750", "GSM467751", "GSM467752", "GSM467753", "GSM467754", "GSM467755", "GSM467756", "GSM467757", "GSM467758", "GSM467759", "GSM467760", "GSM467761", "GSM467762", "GSM467763", "GSM467764", "GSM467765", "GSM467766", "GSM467767", "GSM467768", "GSM467769", "GSM467770"], "sample_count": 198, "group_sizes": null, "group_sizes_basis": null, "platform": "1291", "taxon": "Homo sapiens", "title": "Inherent gene signature of stage II and III colorectal cancer leads in individual recurrence", "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:GSE17538", "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=GSE17538", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17538", "version": null, "note": "We downloaded their normalized mRNA expression data and sample information from the GEO.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded their normalized mRNA expression data and sample information from the GEO.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM437093", "GSM437094", "GSM437095", "GSM437096", "GSM437097", "GSM437098", "GSM437099", "GSM437100", "GSM437101", "GSM437102", "GSM437103", "GSM437104", "GSM437105", "GSM437106", "GSM437107", "GSM437108", "GSM437109", "GSM437110", "GSM437111", "GSM437112", "GSM437113", "GSM437114", "GSM437115", "GSM437116", "GSM437117", "GSM437118", "GSM437119", "GSM437120", "GSM437121", "GSM437122", "GSM437123", "GSM437124", "GSM437125", "GSM437126", "GSM437127", "GSM437128", "GSM437129", "GSM437130", "GSM437131", "GSM437132", "GSM437133", "GSM437134", "GSM437135", "GSM437136", "GSM437137", "GSM437138", "GSM437139", "GSM437140", "GSM437141", "GSM437142", "GSM437143", "GSM437144", "GSM437145", "GSM437146", "GSM437147", "GSM437148", "GSM437149", "GSM437150", "GSM437151", "GSM437152", "GSM437153", "GSM437154", "GSM437155", "GSM437156", "GSM437157", "GSM437158", "GSM437159", "GSM437160", "GSM437161", "GSM437162", "GSM437163", "GSM437164", "GSM437165", "GSM437166", "GSM437167", "GSM437168", "GSM437169", "GSM437170", "GSM437171", "GSM437172", "GSM437173", "GSM437174", "GSM437175", "GSM437176", "GSM437177", "GSM437178", "GSM437179", "GSM437180", "GSM437181", "GSM437182", "GSM437183", "GSM437184", "GSM437185", "GSM437186", "GSM437187", "GSM437188", "GSM437189", "GSM437190", "GSM437191", "GSM437192", "GSM437193", "GSM437194", "GSM437195", "GSM437196", "GSM437197", "GSM437198", "GSM437199", "GSM437200", "GSM437201", "GSM437202", "GSM437203", "GSM437204", "GSM437205", "GSM437206", "GSM437207", "GSM437208", "GSM437209", "GSM437210", "GSM437211", "GSM437212", "GSM437213", "GSM437214", "GSM437215", "GSM437216", "GSM437217", "GSM437218", "GSM437219", "GSM437220", "GSM437221", "GSM437222", "GSM437223", "GSM437224", "GSM437225", "GSM437226", "GSM437227", "GSM437228", "GSM437229", "GSM437230", "GSM437231", "GSM437232", "GSM437233", "GSM437234", "GSM437235", "GSM437236", "GSM437237", "GSM437238", "GSM437239", "GSM437240", "GSM437241", "GSM437242", "GSM437243", "GSM437244", "GSM437245", "GSM437246", "GSM437247", "GSM437248", "GSM437249", "GSM437250", "GSM437251", "GSM437252", "GSM437253", "GSM437254", "GSM437255", "GSM437256", "GSM437257", "GSM437258", "GSM437259", "GSM437260", "GSM437261", "GSM437262", "GSM437263", "GSM437264", "GSM437265", "GSM437266", "GSM437267", "GSM437268", "GSM437269", "GSM437270", "GSM437271", "GSM437272", "GSM437273", "GSM437274", "GSM437275", "GSM437276", "GSM437277", "GSM437278", "GSM437279", "GSM437280", "GSM437281", "GSM437282", "GSM437283", "GSM437284", "GSM437285", "GSM437286", "GSM437287", "GSM437288", "GSM437289", "GSM437290", "GSM437291", "GSM437292", "GSM437293", "GSM437294", "GSM437295", "GSM437296", "GSM437297", "GSM437298", "GSM437299", "GSM437300", "GSM437301", "GSM437302", "GSM437303", "GSM437304", "GSM437305", "GSM437306", "GSM437307", "GSM437308", "GSM437309", "GSM437310", "GSM437311", "GSM437312", "GSM437313", "GSM437314", "GSM437315", "GSM437316", "GSM437317", "GSM437318", "GSM437319", "GSM437320", "GSM437321", "GSM437322", "GSM437323", "GSM437324", "GSM472192", "GSM472193", "GSM472194", "GSM472195", "GSM472196", "GSM472197", "GSM472198", "GSM472199", "GSM472200", "GSM472201", "GSM472202", "GSM472203"], "sample_count": 244, "group_sizes": null, "group_sizes_basis": null, "platform": "570;1261", "taxon": "Mus musculus; Homo sapiens", "title": "Experimentally Derived Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients", "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:22348113:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:790221deb00327098480b7cd863399e68db7ae0277b597df03db779698b9459e", "bytes": 1005, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#pone-0031587-t001", "version": null, "note": "The datasets for computation analysis after preprocessing and quality control.", "structure": {"pmcid": "PMC3278467", "section_index": 3, "section_title": "Search strategy for mRNA datasets from GEO", "row_count": 8, "column_count": 8}, "table": {"label": "Table 1", "caption": "The datasets for computation analysis after preprocessing and quality control.", "rows": [["Study", "Stage", "Number of sample", "Follow-up period", "Platform", "Number of Probes", "Published"], ["", "", "Recurrence/Non-recurrence", "(months)", "", "All", "After QC", "years"], ["GSE12032", "II", "30/62", ">45.9", "AceGene Human Oligo Chip 30 K(GPL1291)", "29640", "9297", "2009a"], ["GSE12032", "III", "47/59", ">45.9", "AceGene Human Oligo Chip 30 K(GPL1291)", "29640", "9297", "2009a"], ["GSE17538", "II", "6/17", "68.6 (median)", "HG-U133Plus 2.0 (GPL570)", "54675", "13594", "2009 [44]"], ["GSE17538", "III", "15/16", "60 (median)", "HG-U133Plus 2.0 (GPL570)", "54675", "13594", "2009 [44]"], ["GSE17181", "II", "16/24", "73 (mean)", "Agilent-014950 CGH Microarray (GPL8841)", "42426", "10630", "2010 [45]"], ["GSE4526", "III", "13/23", "54 (median)", "HG-U133Plus 2.0 (GPL570)", "54675", "13056", "2010 [46]"]], "row_count": 8, "column_count": 8, "numeric_cells": 42, "header_rows": 2, "locator": "section[3]/table-wrap[1]#pone-0031587-t001"}}, {"id": "asset:table:pmid:22348113:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:abef6abf9bc4a8bb216680352a5518ea34f927081eba56d8d731d5c497e53c38", "bytes": 538, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#pone-0031587-t002", "version": null, "note": "Association between microRNAs and CRC recurrence of the stage II and III CRC patients in the different datasets.", "structure": {"pmcid": "PMC3278467", "section_index": 10, "section_title": "Identification of miR-29a and miR-29c as candidate microRNAs for CRC recurrence", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "Association between microRNAs and CRC recurrence of the stage II and III CRC patients in the different datasets.", "rows": [["Stage II", "GSE17181 (n = 40)", "GSE12032 (n = 92)", "GSE17538 (n = 23)"], ["MiR", "p value", "p value", "p value"], ["hsa-miR-29a", "0.08", "<0.01", "0.02"], ["hsa-miR-29c", "0.01", "<0.01", "0.03"], ["hsa-miR-100", "0.04", "<0.01", "0.02"], ["hsa-miR-627", "0.04", "<0.01", "0.02"]], "row_count": 6, "column_count": 4, "numeric_cells": 19, "header_rows": 2, "locator": "section[10]/table-wrap[1]#pone-0031587-t002"}}, {"id": "asset:table:pmid:22348113:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9d442f00af3553494eb0b8148e9266f7c369667e965cea12b2c3027acc673183", "bytes": 726, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#pone-0031587-t003", "version": null, "note": "miR-29a and miR-29c expression levels in our CRC samples of early recurrence and non-early recurrence.", "structure": {"pmcid": "PMC3278467", "section_index": 12, "section_title": "miR-29a and miR-29c expression level in CRC samples", "row_count": 10, "column_count": 5}, "table": {"label": "Table 3", "caption": "miR-29a and miR-29c expression levels in our CRC samples of early recurrence and non-early recurrence.", "rows": [["", "Non-early recurrence", "Early- recurrence", "Crude", "Adjusted"], ["", "n = 27", "n = 41", "", ""], ["", "mean ± sd", "mean ± sd", "p value", "p value†"], ["Age", "68.0±13.0", "65.2±13.9", "0.409", ""], ["Female, n (%)", "11 (40.7)", "17 (41.5)", "0.953", ""], ["stage", "", "", "", ""], ["2", "19 (54.3)", "18 (41.9)", "0.047", ""], ["3", "8 (22.9)", "23 (53.5)", "", ""], ["miR-29a‡", "1.57±0.51", "1.25±0.49", "0.019", "0.020"], ["miR-29c‡", "0.81±0.49", "0.50±0.44", "0.009", "0.009"]], "row_count": 10, "column_count": 5, "numeric_cells": 25, "header_rows": 3, "locator": "section[12]/table-wrap[1]#pone-0031587-t003"}}], "gaps": ["asset:data:geo:GSE12032 not downloaded", "asset:data:geo:GSE12032 licence not read", "asset:data:geo:GSE17538 not downloaded", "asset:data:geo:GSE17538 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "random_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": ["random_effects_pool"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The random effect model showed an effect size of 213.36 (95% CI: 147.38–279.34) for miR-29a and an effect size of 176.91 (95% CI: 111.63–242.18) for miR-29c."}}, {"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"}}], "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": ["random_effects_pool"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_effects."}, "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": ["GSE12032", "GSE17538", "GSE4526 and GSE17181"], "resolved_accessions": ["GSE12032", "GSE17538"], "statements": ["We downloaded their normalized mRNA expression data and sample information from the GEO."], "basis": "The paper names GSE12032, GSE17538 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": ["random_effects_pool"], "assets": ["source:pmid:22348113", "data:geo:GSE12032", "asset:table:pmid:22348113:1", "asset:table:pmid:22348113:2", "asset:table:pmid:22348113:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12032"]}, "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": null}, "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:22348113", "type": "paper", "label": "pmid:22348113"}, {"id": "source:pmid:22348113", "type": "manuscript", "label": "PMID 22348113 full text"}, {"id": "data:geo:GSE12032", "type": "dataset", "label": "GEO GSE12032"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:22348113", "type": "paper", "label": "pmid:22348113"}, {"id": "source:pmid:22348113", "type": "manuscript", "label": "PMID 22348113 full text"}, {"id": "data:geo:GSE12032", "type": "dataset", "label": "GEO GSE12032"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-22348113", "type": "extraction", "used": ["source:pmid:22348113"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12032", "type": "accession_resolution", "used": ["data:geo:GSE12032"], "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:22348113", "parent_hash": "sha256:67e0f12d8fd2e03932149e2a7ba895141efa42bf44f2230cf2fe9494d03f6b56", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE12032 licence not read", "asset:data:geo:GSE12032 not downloaded", "asset:data:geo:GSE17538 licence not read", "asset:data:geo:GSE17538 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": ["rom the computational analysis based on mRNA microarray datasets, indicating that the two microRNAs"], "order_basis": "paper_text_order:2574", "id": "assay:1"}, {"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["random_effects_pool"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The random effect model showed an effect size of 213.36 (95% CI: 147.38–279.34) for miR-29a and an effect size of 176.91 (95% CI: 111.63–242.18) for miR-29c."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}