Down-regulation and clinical significance of miR-7-2-3p in papillary thyroid carcinoma with multiple detecting methods.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31538956", "kind": "science-record", "revision": 2, "content_hash": "sha256:3b1c449dc7e7083676ed2251f74e5731c3e5621940d48866dca036ed2aae5b7a", "created_at": "2026-11-01T17:33:04Z", "updated_at": "2026-11-01T18:51:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Down-regulation and clinical significance of miR-7-2-3p in papillary thyroid carcinoma with multiple detecting methods.", "doi": "10.1049/iet-syb.2019.0025", "pmid": "31538956", "authors": ["Hua-Yu Wu", "Yi Wei", "Shang-Ling Pan"], "journal": "IET systems biology", "year": 2019, "abstract": "Altered miRNA expression participates in the biological progress of thyroid carcinoma and functions as a diagnostic marker or therapeutic agent. However, the role of miR-7-2-3p is currently unclear. The authors' study was the first investigation of miR-7-2-3p expression level and diagnostic ability in several public databases. Potential target genes were obtained from DIANA Tools, and function enrichment analysis was then performed. Furthermore, the authors examined expression levels of potential targets in the Human Protein Atlas (HPA) and the Cancer Genome Atlas (TCGA). Finally, the potential transcription factors (TFs) were predicted by JASPAR. TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR-7-2-3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non-tumour tissues, while its expression in E-MATB-736 showed no remarkable difference. Function enrichment analysis showed that 698 genes were enriched in pathways, including pathways in cancer, and glioma. CCND1, GSK3B, and ITGAV of pathways in cancer were inverse correlations with miR-7-2-3p in both post-transcription and protein levels. According to the TF prediction, the prospective upstream TFs of miR-7-2-3p were ISX, SPI1, PRRX1, and BARX1. MiR-7-2-3p was significantly down-regulated and may act on PTC progression by crucial pathways. However, the mechanisms of miR-7-2-3p need further investigation.", "claims": [{"id": "claim-data-access", "statement": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31538956", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:31538956"], "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:GSE40807"], "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:GSE40807"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31538956", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1049/iet-syb.2019.0025", "sha256": "sha256:3e429f72793daf1131c7f4e07b2fb474982bae9d0b48ba074dd899158a4c9190", "bytes": 1444, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1049/iet-syb.2019.0025", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8687168", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE40807", "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=GSE40807", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40807", "version": null, "note": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1002105", "GSM1002106", "GSM1002107", "GSM1002108", "GSM1002109", "GSM1002110", "GSM1002111", "GSM1002112", "GSM1002113", "GSM1002114", "GSM1002115", "GSM1002116", "GSM1002117", "GSM1002118", "GSM1002119", "GSM1002120", "GSM1002121", "GSM1002122", "GSM1002123", "GSM1002124", "GSM1002125", "GSM1002126", "GSM1002127", "GSM1002128", "GSM1002129", "GSM1002130", "GSM1002131", "GSM1002132", "GSM1002133", "GSM1002134", "GSM1002135", "GSM1002136", "GSM1002137", "GSM1002138", "GSM1002139", "GSM1002140", "GSM1002141", "GSM1002142", "GSM1002143", "GSM1002144", "GSM1002145", "GSM1002146", "GSM1002147", "GSM1002148", "GSM1002149", "GSM1002150", "GSM1002151", "GSM1002152", "GSM1002153", "GSM1002154", "GSM1002155", "GSM1002156", "GSM1002157", "GSM1002158", "GSM1002159", "GSM1002160", "GSM1002161", "GSM1002162", "GSM1002163", "GSM1002164", "GSM1002165", "GSM1002166", "GSM1002167", "GSM1002168", "GSM1002169", "GSM1002170", "GSM1002171", "GSM1002172", "GSM1002173", "GSM1002174", "GSM1002175", "GSM1002176", "GSM1002177", "GSM1002178", "GSM1002179", "GSM1002180", "GSM1002181", "GSM1002182", "GSM1002183", "GSM1002184"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "8227", "taxon": "Homo sapiens", "title": "MiRNA expression profiling in human medullary thyroid carcinoma", "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:GSE55780", "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=GSE55780", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE55780", "version": null, "note": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1345985", "GSM1345986", "GSM1345987", "GSM1345988", "GSM1345989", "GSM1345990", "GSM1345991", "GSM1345992", "GSM1345993", "GSM1345994", "GSM1345995", "GSM1345996"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "6101", "taxon": "Rattus norvegicus", "title": "Hippocampal neurons, Illumina experiments", "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:GSE62054", "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=GSE62054", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62054", "version": null, "note": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1519019", "GSM1519020", "GSM1519021", "GSM1519022", "GSM1519023", "GSM1519024", "GSM1519025", "GSM1519026", "GSM1519027", "GSM1519028", "GSM1519029", "GSM1519030", "GSM1519031", "GSM1519032", "GSM1519033", "GSM1519034", "GSM1519035", "GSM1519036", "GSM1519037", "GSM1519038", "GSM1519039", "GSM1519040", "GSM1519041", "GSM1519042", "GSM1519043"], "sample_count": 25, "group_sizes": null, "group_sizes_basis": null, "platform": "8179", "taxon": "Homo sapiens", "title": "A two miRNA classifier differentiates follicular thyroid carcinomas from follicular thyroid adenomas", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE73182", "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=GSE73182", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73182", "version": null, "note": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1888201", "GSM1888202", "GSM1888203", "GSM1888204", "GSM1888205", "GSM1888206", "GSM1888207", "GSM1888208", "GSM1888209", "GSM1888210", "GSM1888211", "GSM1888212", "GSM1888213", "GSM1888214", "GSM1888215", "GSM1888216", "GSM1888217", "GSM1888218", "GSM1888219", "GSM1888220", "GSM1888221", "GSM1888222", "GSM1888223", "GSM1888224"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "20194", "taxon": "Homo sapiens", "title": "miRNA expression profiling of snap-frozen primary papillary thyroid carcinomas (PTC) and normal thyroids", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE40807 not downloaded", "asset:data:geo:GSE40807 licence not read", "asset:data:geo:GSE55780 not downloaded", "asset:data:geo:GSE55780 licence not read", "asset:data:geo:GSE62054 not downloaded", "asset:data:geo:GSE62054 licence not read", "asset:data:geo:GSE73182 not downloaded", "asset:data:geo:GSE73182 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE62054", "GSE73182", "GSE40807", "GSE55780"], "resolved_accessions": ["GSE62054", "GSE73182", "GSE40807", "GSE55780"], "statements": ["TCGA, GSE62054, GSE73182, GSE40807, and GSE55780 revealed that miR‐7‐2‐3p expression in papillary thyroid carcinoma (PTC) tissues was notably lower compared with non‐tumour tissues, while its expression in E‐MATB‐736 showed no remarkable difference."], "basis": "The paper names GSE62054, GSE73182, GSE40807, GSE55780 in GSE62054 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31538956", "data:geo:GSE40807"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE40807"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:58:45Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1980, "completion_tokens": 1825, "cached_tokens": 128}}, "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:31538956", "type": "paper", "label": "pmid:31538956"}, {"id": "source:pmid:31538956", "type": "manuscript", "label": "PMID 31538956 full text"}, {"id": "data:geo:GSE40807", "type": "dataset", "label": "GEO GSE40807"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31538956", "type": "paper", "label": "pmid:31538956"}, {"id": "source:pmid:31538956", "type": "manuscript", "label": "PMID 31538956 full text"}, {"id": "data:geo:GSE40807", "type": "dataset", "label": "GEO GSE40807"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31538956", "type": "extraction", "used": ["source:pmid:31538956"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE40807", "type": "accession_resolution", "used": ["data:geo:GSE40807"], "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:31538956", "parent_hash": "sha256:9553ace2f08495604009f65ccf3414a297d304ff345efe553aa139cfc944c9b7", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE40807 licence not read", "asset:data:geo:GSE40807 not downloaded", "asset:data:geo:GSE55780 licence not read", "asset:data:geo:GSE55780 not downloaded", "asset:data:geo:GSE62054 licence not read", "asset:data:geo:GSE62054 not downloaded", "asset:data:geo:GSE73182 licence not read", "asset:data:geo:GSE73182 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"]}