Two GEO MicroRNA Expression Profile Based High-Throughput Screen to Identify MicroRNA-31-3p Regulating Growth of Medullary Thyroid Carcinoma Cell by Targeting RASA2.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31298226", "kind": "science-record", "revision": 9, "content_hash": "sha256:4122a6d322c5716417173748ae0331746c08ecb10f15536442b3eb9ca34d9eda", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T22:44:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Two GEO MicroRNA Expression Profile Based High-Throughput Screen to Identify MicroRNA-31-3p Regulating Growth of Medullary Thyroid Carcinoma Cell by Targeting RASA2.", "doi": "10.12659/MSM.916815", "pmid": "31298226", "authors": ["Mei Jiang", "Xin Shi", "Hua Zhu", "Wu Wei", "Jinyan Li"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2019, "abstract": "BACKGROUND Medullary thyroid carcinoma (MTC), a rare type of thyroid cancer, is a big challenge in clinical treatment. However, the pathogenesis of MTC remains poorly understand. MicroRNAs (miRNAs) were previously demonstrated to be involved in the pathogenesis of MTC, however, the roles of majority of miRNAs in MTC are still undetermined. MATERIAL AND METHODS Two GEO miRNA expression profiles (GSE40807, GSE97070) were downloaded, and the differentially expressed miRNAs (DEmiRNAs) of GSE40807 and GSE97070 were analyzed by bioinformatics methods. Expressions of miRNAs were detected by quantitative real-time polymerase chain reaction; cell proliferation was examined through Cell Counting Kit-8, colony formation and in vivo tumor growth assays; the interaction between miRNA and mRNA was verified by dual-luciferase reporter assay; functional analysis of target genes was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID, www.david.ncifcrf.gov) software. RESULTS Ten miRNAs were identified to be dysregulated in both GSE40807 and GSE97070 datasets, and miR-31-3p showed the highest change fold (Log fold change=-3.460625 in GSE40807 and Log fold change=-0.07084374 in GSE97070). MiR-31-3p expression was significantly downregulated in MTC, and low miR-31-3p expression showed a poor prognosis relative to high miR-31-3p expression (P<0.05). Functionally, miR-31-3p inhibited MTC cell proliferation in vitro and in vivo. Functional analysis also showed that the target genes of miR-31-3p were involved in numerous of biochemical processes and pathways, of which Ras signaling pathway was selected for further study. RASA2, overexpressed in MTC, were negatively regulated by miR-31-3p. In addition, we found that knockdown of RASA2 inhibited MTC cell proliferation. CONCLUSIONS Reduced expression level of miR-31-3p might play a key role in the tumorigenesis of MTC by targeting critical pathways, especially Ras signaling pathway.", "claims": [{"id": "claim-method", "statement": "Data were expressed as mean ±SEM in this study, One-way analysis of variance, conducted using SPSS v20 software (IBM Corp., Armonk, NY, USA), was applied to compare the difference between groups, P value less than 0.05 was considered as significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31298226", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "Data were expressed as mean ±SEM in this study, One-way analysis of variance, conducted using SPSS v20 software (IBM Corp., Armonk, NY, USA), was applied to compare the difference between groups, P value less than 0.05 was considered as significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31298226", "locator": "sections[4] \"Microarray datasets\" paragraph 2", "quote": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples."}], "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:31298226"], "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:31298226", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.916815", "sha256": "sha256:6f2260793523d0013195388af3099e434b43ad2ab4f4bec5518dc42fa4ab53c0", "bytes": 36465, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.916815", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6642674", "source": "europe_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": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples.", "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:GSE97070", "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=GSE97070", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE97070", "version": null, "note": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2550963", "GSM2550964", "GSM2550965", "GSM2550966", "GSM2550967", "GSM2550968", "GSM2550969", "GSM2550970", "GSM2550971", "GSM2550972", "GSM2550973", "GSM2550974", "GSM2550975", "GSM2550976", "GSM2550977", "GSM2550978", "GSM2550979", "GSM2550980", "GSM2550981", "GSM2550982"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "18402", "taxon": "Homo sapiens", "title": "microRNA profile of human medullary thyroid cancer", "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:GSE97070 not downloaded", "asset:data:geo:GSE97070 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Data were expressed as mean ±SEM in this study, One-way analysis of variance, conducted using SPSS v20 software (IBM Corp., Armonk, NY, USA), was applied to compare the difference between groups, P value less than 0.05 was considered as significant."}}], "targets": [], "gaps": []}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE40807", "GSE97070"], "resolved_accessions": ["GSE40807", "GSE97070"], "statements": ["The miRNA datasets (GSE40807 and GSE97070) were searched and downloaded from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE40807 was conducted through GPL8227 platforms (Agilent-019118 Human miRNA Microarray 2.0 G4470B) and consisted of 80 samples."], "basis": "The paper names GSE40807, GSE97070 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:31298226", "data:geo:GSE40807"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE40807"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:36Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 33299, "completion_tokens": 1673, "cached_tokens": 784}}, "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:31298226", "type": "paper", "label": "pmid:31298226"}, {"id": "source:pmid:31298226", "type": "manuscript", "label": "PMID 31298226 full text"}, {"id": "data:geo:GSE40807", "type": "dataset", "label": "GEO GSE40807"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31298226", "type": "paper", "label": "pmid:31298226"}, {"id": "source:pmid:31298226", "type": "manuscript", "label": "PMID 31298226 full text"}, {"id": "data:geo:GSE40807", "type": "dataset", "label": "GEO GSE40807"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31298226", "type": "extraction", "used": ["source:pmid:31298226"], "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:31298226", "parent_hash": "sha256:1850c1b887e67dea6ba68773c374cf3ee90388a3ab4f130722aeb59777a250e5", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE40807 licence not read", "asset:data:geo:GSE40807 not downloaded", "asset:data:geo:GSE97070 licence not read", "asset:data:geo:GSE97070 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["gh Cell Counting Kit-8, colony formation and in vivo tumor growth assays; the interaction between", "nhibited MTC cell proliferation in vitro and in vivo. Functional analysis also showed that the ta"], "order_basis": "paper_text_order:844", "id": "assay:1"}, {"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": ["ted by miR-31-3p. In addition, we found that knockdown of RASA2 inhibited MTC cell proliferation. C", "levels of RASA1, RASA2 and RASA4 of TT cells transfected with miR-31-3p mimic or its control were mea"], "order_basis": "paper_text_order:1881", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Data were expressed as mean ±SEM in this study, One-way analysis of variance, conducted using SPSS v20 software (IBM Corp., Armonk, NY, USA), was applied to compare the difference between groups, P value less than 0.05 was considered as significant."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}