Identification of microRNA-mRNA regulatory networks and pathways related to retinoblastoma across human and mouse.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32399402", "kind": "science-record", "revision": 4, "content_hash": "sha256:297d248835ff425703314b9efce77cfa9bb893cc4d07e0da48e98343fdcf10c6", "created_at": "2026-11-01T17:33:39Z", "updated_at": "2026-11-01T22:01:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of microRNA-mRNA regulatory networks and pathways related to retinoblastoma across human and mouse.", "doi": "10.18240/ijo.2020.04.02", "pmid": "32399402", "authors": ["Rui Tian", "He Zou", "Lu-Fei Wang", "Mei-Jiao Song", "Lu Liu", "Hui Zhang"], "journal": "International journal of ophthalmology", "year": 2020, "abstract": "AIM: To explore the mRNA and pathways related to retinoblastoma (RB) genesis and development.\nMETHODS: Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database. Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction (PPI) network construction and gene enrichment analysis. Disease-related miRNAs and pathways were retrieved from miR2Disease database and Comparative Toxicogenomics Database (CTD), respectively.\nRESULTS: A total of 352 homologous genes were identified. Two pathways including \"cell cycle\" and \"pathway in cancer\" in CTD and enrichment analysis were identified and seven miRNAs (including hsa-miR-373, hsa-miR-34a, hsa-miR-129, hsa-miR-494, hsa-miR-503, hsa-let-7 and hsa-miR-518c) were associated with RB. miRNAs modulate \"cell cycle\" and \"pathway in cancer\" pathways via regulating 13 genes (including CCND1, CDC25C, E2F2, CDKN2D and TGFB2).\nCONCLUSION: These results suggest that these miRNAs play crucial roles in RB genesis through \"cell cycle\" and \"pathway in cancer\" pathways by regulating their targets including CCND1, CDC25C, E2F2 and CDKN2D.", "claims": [{"id": "claim-method", "statement": "Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction (PPI) network construction and gene enrichment analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32399402", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction (PPI) network construction and gene enrichment analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32399402", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 352 homologous genes were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:32399402", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 352 homologous genes were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 352 homologous genes were identified.", "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:32399402"], "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:GSE29683"], "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:GSE29683"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32399402", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18240/ijo.2020.04.02", "sha256": "sha256:49cb3456316954a372c1a3287c010fc620b190967eb37f2c57bd43e137b2479e", "bytes": 1140, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18240/ijo.2020.04.02", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7137714", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29683", "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=GSE29683", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29683", "version": null, "note": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM736228", "GSM736229", "GSM736230", "GSM736231", "GSM736232", "GSM736233", "GSM736234", "GSM736235", "GSM736236", "GSM736237", "GSM736238", "GSM736239", "GSM736240", "GSM736241", "GSM736242", "GSM736243", "GSM736244", "GSM736245", "GSM736246", "GSM736247", "GSM736248", "GSM736249", "GSM736250", "GSM736251", "GSM736252", "GSM736253", "GSM736254", "GSM736255", "GSM736256", "GSM736257", "GSM736258", "GSM736259", "GSM736260", "GSM736261", "GSM736262", "GSM736263", "GSM736264", "GSM736265", "GSM736266", "GSM736267", "GSM736268", "GSM736269", "GSM736270", "GSM736271", "GSM736272", "GSM736273", "GSM736274", "GSM736275", "GSM736276", "GSM736277", "GSM736278", "GSM736279", "GSM736280", "GSM736281", "GSM736282", "GSM736283", "GSM736284", "GSM736285", "GSM736286", "GSM736287", "GSM736288", "GSM736289"], "sample_count": 62, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Coexpression of Normally Incompatible Developmental Pathways in Retinoblastoma Genesis [human tumor/cell line data]", "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:GSE29685", "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=GSE29685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29685", "version": null, "note": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM736310", "GSM736311", "GSM736312", "GSM736313", "GSM736314", "GSM736315", "GSM736316", "GSM736317", "GSM736318", "GSM736319", "GSM736320", "GSM736321", "GSM736322", "GSM736323", "GSM736324", "GSM736325", "GSM736326", "GSM736327", "GSM736328", "GSM736329", "GSM736330", "GSM736331", "GSM736332", "GSM736333", "GSM736334", "GSM736335", "GSM736336", "GSM736337", "GSM736338", "GSM736339", "GSM736340", "GSM736341", "GSM736342", "GSM736343", "GSM736344", "GSM736345", "GSM736346", "GSM736347", "GSM736348", "GSM736349", "GSM736350", "GSM736351", "GSM736352", "GSM736353", "GSM736354", "GSM736355", "GSM736356", "GSM736357", "GSM736358", "GSM736359", "GSM736360", "GSM736361", "GSM736362", "GSM736363", "GSM736364", "GSM736365", "GSM736366", "GSM736367", "GSM736368", "GSM736369", "GSM736370", "GSM736371", "GSM736372", "GSM736373", "GSM736374", "GSM736375", "GSM736376", "GSM736377", "GSM736378", "GSM736379", "GSM736380", "GSM736381", "GSM736382", "GSM736383", "GSM736384", "GSM736385", "GSM736386", "GSM736387", "GSM736388", "GSM736389", "GSM736390", "GSM736391", "GSM736392", "GSM736393", "GSM736394", "GSM736395", "GSM736396", "GSM736397", "GSM736398", "GSM736399", "GSM736400", "GSM736401", "GSM736402", "GSM736403", "GSM736404", "GSM736405", "GSM736406", "GSM736407", "GSM736408", "GSM736409", "GSM736410", "GSM736411", "GSM736412", "GSM736413", "GSM736414", "GSM736415", "GSM736416", "GSM736417", "GSM736418", "GSM736419", "GSM736420", "GSM736421", "GSM736422", "GSM736423", "GSM736424", "GSM736425", "GSM736426", "GSM736427", "GSM736428", "GSM736429", "GSM736430", "GSM736431", "GSM736432", "GSM736433", "GSM736434", "GSM736435", "GSM736436", "GSM736437", "GSM736438", "GSM736439", "GSM736440", "GSM736441"], "sample_count": 132, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Coexpression of Normally Incompatible Developmental Pathways in Retinoblastoma Genesis [mouse model data]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE29683 not downloaded", "asset:data:geo:GSE29683 licence not read", "asset:data:geo:GSE29685 not downloaded", "asset:data:geo:GSE29685 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction (PPI) network construction and gene enrichment analysis."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE29683", "GSE29685"], "resolved_accessions": ["GSE29683", "GSE29685"], "statements": ["Microarray datasets GSE29683 (human) and GSE29685 (mouse) were downloaded from NCBI GEO database."], "basis": "The paper names GSE29683, GSE29685 in NCBI GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:32399402", "data:geo:GSE29683"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29683"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:59:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 1926, "completion_tokens": 1033, "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:32399402", "type": "paper", "label": "pmid:32399402"}, {"id": "source:pmid:32399402", "type": "manuscript", "label": "PMID 32399402 full text"}, {"id": "data:geo:GSE29683", "type": "dataset", "label": "GEO GSE29683"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32399402", "type": "paper", "label": "pmid:32399402"}, {"id": "source:pmid:32399402", "type": "manuscript", "label": "PMID 32399402 full text"}, {"id": "data:geo:GSE29683", "type": "dataset", "label": "GEO GSE29683"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32399402", "type": "extraction", "used": ["source:pmid:32399402"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29683", "type": "accession_resolution", "used": ["data:geo:GSE29683"], "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:32399402", "parent_hash": "sha256:c337c4d61ffa3d10f3dd4fe7957cd019bc6f14bc27a58c4c292f469d06829c47", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE29683 licence not read", "asset:data:geo:GSE29683 not downloaded", "asset:data:geo:GSE29685 licence not read", "asset:data:geo:GSE29685 not downloaded", "execution.not_run", "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": ["stoma (RB) genesis and development. METHODS: Microarray datasets GSE29683 (human) and GSE29685 (mous"], "order_basis": "paper_text_order:173", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction (PPI) network construction and gene enrichment analysis."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}