Construction of miRNA-mRNA-TF Regulatory Network for Diagnosis of Gastric Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34840985", "kind": "science-record", "revision": 3, "content_hash": "sha256:b32954235ef70f69d13792a370a7a1887fea91fb439dfbd124b1cccdc118e678", "created_at": "2026-11-01T17:36:32Z", "updated_at": "2026-11-01T21:26:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of miRNA-mRNA-TF Regulatory Network for Diagnosis of Gastric Cancer.", "doi": "10.1155/2021/9121478", "pmid": "34840985", "authors": ["Zhenjie Fu", "Yuqin Xu", "Yan Chen", "Hang Lv", "Guiping Chen", "Yitao Chen"], "journal": "BioMed research international", "year": 2021, "abstract": "Gastric cancer (GC), as an epidemic cancer worldwide, has more than 1 million new cases and an estimated 769,000 deaths worldwide in 2020, ranking fifth and fourth in global morbidity and mortality. In mammals, both miRNAs and transcription factors (TFs) play a partial role in gene expression regulation. The mRNA expression profile and miRNA expression profile of GEO database were screened by GEO2R for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Then, DAVID annotated the functions of DEGs to understand the functions played in biological processes. The prediction of potential target genes of miRNA and key TFs of mRNA was performed by mipathDB V2.0 and CHEA3, respectively, and the gene list comparison was performed to look for overlapping genes coregulated by key TFs and DEMs. Finally, the obtained miRNAs, TF, and overlapping genes were used to construct the miRNA-mRNA-TF regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively. Through database prediction and gene list comparison, it was found that among the 199 downregulated DEGs, 61, 71, and 69 genes were the potential targets of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p, respectively. 199 downregulated DEGs were used as the gene list for the prediction of key TFs, and the results showed that RFX6 ranked the highest. The potential target overlap genes of miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p were 4 genes (SH3GL2, ATP4B, CTSE, and SORBS2), 7 genes (SLC7A8, RNASE4, ESRRG, PGC, MUC6, Fam3B, and FMO5), and 6 genes (CHGA, PDK4, TMPRSS2, CLIC6, GPX3, and PSCA), respectively. Finally, we constructed a miRNA-mRNA-TF regulatory network based on the above 17 mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression of RFX6 was downregulated in GC tissues. These identified miRNAs, mRNAs, and TF have a certain reference value for further exploration of the regulatory mechanism of GC.", "claims": [{"id": "claim-method", "statement": "GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) is a software based on GEO database to perform differential analysis on expression profile chips.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34840985", "locator": "sections[4] \"2.2. Identification of DEGs and DEMs\" paragraph 2", "quote": "GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) is a software based on GEO database to perform differential analysis on expression profile chips."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34840985", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34840985", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "76 upregulated DEGs, 199 downregulated DEGs, and 3 upregulated miRNAs (miR-199a-3p/miR-199b-3p, miR-125b-5p, and miR-199a-5p) were identified from the expression profiles of mRNA (GSE26899, GSE29998, GSE51575, and GSE13911) and miRNA (GSE93415), respectively.", "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:34840985"], "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:GSE13911"], "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:GSE13911"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34840985", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/9121478", "sha256": "sha256:20ecd183481b446372dbce3c6587515e31a3217b89a9009a8d2cc7af0512180e", "bytes": 27680, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/9121478", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8616677", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13911", "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=GSE13911", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13911", "version": null, "note": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM350411", "GSM350412", "GSM350413", "GSM350414", "GSM350415", "GSM350416", "GSM350417", "GSM350418", "GSM350419", "GSM350420", "GSM350421", "GSM350422", "GSM350423", "GSM350424", "GSM350425", "GSM350426", "GSM350427", "GSM350428", "GSM350429", "GSM350430", "GSM350431", "GSM350432", "GSM350433", "GSM350434", "GSM350435", "GSM350436", "GSM350437", "GSM350438", "GSM350439", "GSM350440", "GSM350441", "GSM350442", "GSM350443", "GSM350444", "GSM350445", "GSM350446", "GSM350447", "GSM350448", "GSM350449", "GSM350450", "GSM350451", "GSM350452", "GSM350453", "GSM350454", "GSM350455", "GSM350456", "GSM350457", "GSM350458", "GSM350459", "GSM350460", "GSM350461", "GSM350462", "GSM350463", "GSM350464", "GSM350465", "GSM350466", "GSM350467", "GSM350468", "GSM350469", "GSM350470", "GSM350471", "GSM350472", "GSM350473", "GSM350474", "GSM350475", "GSM350476", "GSM350477", "GSM350478", "GSM350479"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from primary gastric tumors (MSI and MSS) and adjacent normal samples", "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:GSE26899", "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=GSE26899", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26899", "version": null, "note": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662374", "GSM662375", "GSM662376", "GSM662377", "GSM662378", "GSM662379", "GSM662380", "GSM662381", "GSM662382", "GSM662383", "GSM662384", "GSM662385", "GSM662386", "GSM662387", "GSM662388", "GSM662389", "GSM662390", "GSM662391", "GSM662392", "GSM662393", "GSM662394", "GSM662395", "GSM662396", "GSM662397", "GSM662398", "GSM662399", "GSM662400", "GSM662401", "GSM662402", "GSM662403", "GSM662404", "GSM662405", "GSM662406", "GSM662407", "GSM662408", "GSM662409", "GSM662410", "GSM662411", "GSM662412", "GSM662413", "GSM662414", "GSM662415", "GSM662416", "GSM662417", "GSM662418", "GSM662419", "GSM662420", "GSM662421", "GSM662422", "GSM662423", "GSM662424", "GSM662425", "GSM662426", "GSM662427", "GSM662428", "GSM662429", "GSM662430", "GSM662431", "GSM662432", "GSM662433", "GSM662434", "GSM662435", "GSM662436", "GSM662437", "GSM662438", "GSM662439", "GSM662440", "GSM662441", "GSM662442", "GSM662443", "GSM662444", "GSM662445", "GSM662446", "GSM662447", "GSM662448", "GSM662449", "GSM662450", "GSM662451", "GSM662452", "GSM662453", "GSM662454", "GSM662455", "GSM662456", "GSM662457", "GSM662458", "GSM662459", "GSM662460", "GSM662461", "GSM662462", "GSM662463", "GSM662464", "GSM662465", "GSM662466", "GSM662467", "GSM662468", "GSM662469", "GSM662470", "GSM662471", "GSM662472", "GSM662473", "GSM662474", "GSM662475", "GSM662476", "GSM662477", "GSM662478", "GSM662479", "GSM662480", "GSM662481"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Characterization of gene expression profiles of gastric cancer in the Korea University cohort", "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:GSE29998", "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=GSE29998", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29998", "version": null, "note": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM742395", "GSM742396", "GSM742397", "GSM742398", "GSM742399", "GSM742400", "GSM742401", "GSM742402", "GSM742403", "GSM742404", "GSM742405", "GSM742406", "GSM742407", "GSM742408", "GSM742409", "GSM742410", "GSM742411", "GSM742412", "GSM742413", "GSM742414", "GSM742415", "GSM742416", "GSM742417", "GSM742418", "GSM742419", "GSM742420", "GSM742421", "GSM742422", "GSM742423", "GSM742424", "GSM742425", "GSM742426", "GSM742427", "GSM742428", "GSM742429", "GSM742430", "GSM742431", "GSM742432", "GSM742433", "GSM742434", "GSM742435", "GSM742436", "GSM742437", "GSM742438", "GSM742439", "GSM742440", "GSM742441", "GSM742442", "GSM742443", "GSM742444", "GSM742445", "GSM742446", "GSM742447", "GSM742448", "GSM742449", "GSM742450", "GSM742451", "GSM742452", "GSM742453", "GSM742454", "GSM742455", "GSM742456", "GSM742457", "GSM742458", "GSM742459", "GSM742460", "GSM742461", "GSM742462", "GSM742463", "GSM742464", "GSM742465", "GSM742466", "GSM742467", "GSM742468", "GSM742469", "GSM742470", "GSM742471", "GSM742472", "GSM742473", "GSM742474", "GSM742475", "GSM742476", "GSM742477", "GSM742478", "GSM742479", "GSM742480", "GSM742481", "GSM742482", "GSM742483", "GSM742484", "GSM742485", "GSM742486", "GSM742487", "GSM742488", "GSM742489", "GSM742490", "GSM742491", "GSM742492", "GSM742493"], "sample_count": 99, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine [Illumina mRNA expression array data]", "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:GSE51575", "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=GSE51575", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51575", "version": null, "note": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1248612", "GSM1248613", "GSM1248614", "GSM1248615", "GSM1248616", "GSM1248617", "GSM1248618", "GSM1248619", "GSM1248620", "GSM1248621", "GSM1248622", "GSM1248623", "GSM1248624", "GSM1248625", "GSM1248626", "GSM1248627", "GSM1248628", "GSM1248629", "GSM1248630", "GSM1248631", "GSM1248632", "GSM1248633", "GSM1248634", "GSM1248635", "GSM1248636", "GSM1248637", "GSM1248638", "GSM1248639", "GSM1248640", "GSM1248641", "GSM1248642", "GSM1248643", "GSM1248644", "GSM1248645", "GSM1248646", "GSM1248647", "GSM1248648", "GSM1248649", "GSM1248650", "GSM1248651", "GSM1248652", "GSM1248653", "GSM1248654", "GSM1248655", "GSM1248656", "GSM1248657", "GSM1248660", "GSM1248661", "GSM1248662", "GSM1248663", "GSM1248664", "GSM1248665"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "13607", "taxon": "Homo sapiens", "title": "mRNA Expression Profiling in EBV-postive Gastric Carcinoma and EBV-negative GC in comparison with their normal mucosa tissue", "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:GSE93415", "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=GSE93415", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE93415", "version": null, "note": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2452858", "GSM2452859", "GSM2452860", "GSM2452861", "GSM2452862", "GSM2452863", "GSM2452864", "GSM2452865", "GSM2452866", "GSM2452867", "GSM2452868", "GSM2452869", "GSM2452870", "GSM2452871", "GSM2452872", "GSM2452873", "GSM2452874", "GSM2452875", "GSM2452876", "GSM2452877", "GSM2452878", "GSM2452879", "GSM2452880", "GSM2452881", "GSM2452882", "GSM2452883", "GSM2452884", "GSM2452885", "GSM2452886", "GSM2452887", "GSM2452888", "GSM2452889", "GSM2452890", "GSM2452891", "GSM2452892", "GSM2452893", "GSM2452894", "GSM2452895", "GSM2452896", "GSM2452897"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "19071", "taxon": "Human alphaherpesvirus 1; Human alphaherpesvirus 2; Cytomegalovirus; Lymphocryptovirus; Betapolyomavirus macacae; Homo sapiens; Rhadinovirus; Human immunodeficiency virus 1; Merkel cell polyomavirus; JC polyomavirus; Betapolyomavirus hominis", "title": "MicroRNA profiling of gastric 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:GSE13911 not downloaded", "asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE93415 not downloaded", "asset:data:geo:GSE93415 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) is a software based on GEO database to perform differential analysis on expression profile chips."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE26899", "GSE29998", "GSE51575", "GSE13911", "GSE93415"], "resolved_accessions": ["GSE26899", "GSE29998", "GSE51575", "GSE13911", "GSE93415"], "statements": ["The datasets of GSE26899, GSE29998, GSE51575, GSE13911, and GSE93415 were downloaded from the GEO database."], "basis": "The paper names GSE26899, GSE29998, GSE51575, GSE13911, GSE93415 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": ["pathway_enrich"], "assets": ["source:pmid:34840985", "data:geo:GSE13911"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13911"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:09:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9183, "completion_tokens": 1831, "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:34840985", "type": "paper", "label": "pmid:34840985"}, {"id": "source:pmid:34840985", "type": "manuscript", "label": "PMID 34840985 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34840985", "type": "paper", "label": "pmid:34840985"}, {"id": "source:pmid:34840985", "type": "manuscript", "label": "PMID 34840985 full text"}, {"id": "data:geo:GSE13911", "type": "dataset", "label": "GEO GSE13911"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34840985", "type": "extraction", "used": ["source:pmid:34840985"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13911", "type": "accession_resolution", "used": ["data:geo:GSE13911"], "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:34840985", "parent_hash": "sha256:38e2aca2b1a4220241227616ade983a61809973fc1225e6901a4abb680aa3673", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE13911 licence not read", "asset:data:geo:GSE13911 not downloaded", "asset:data:geo:GSE26899 licence not read", "asset:data:geo:GSE26899 not downloaded", "asset:data:geo:GSE29998 licence not read", "asset:data:geo:GSE29998 not downloaded", "asset:data:geo:GSE51575 licence not read", "asset:data:geo:GSE51575 not downloaded", "asset:data:geo:GSE93415 licence not read", "asset:data:geo:GSE93415 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["TF regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs", "17 mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression", "regulatory network, which was verified by RT-qPCR. 76 upregulated DEGs, 199 downregulated DEGs", "mRNAs, 3 miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression"], "order_basis": "paper_text_order:1000", "id": "assay:1"}, {"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": ["miRNAs, and 1 TF and verified by RT-qPCR and western blot results that the expression of RFX6 was down"], "order_basis": "paper_text_order:2037", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["pathway enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}