Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA-mRNA pairs in cisplatin-resistant ovarian cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33892654", "kind": "science-record", "revision": 8, "content_hash": "sha256:454753adee3c845d79dfcfa4fb9798efeeb0411187332490306a502d286afd7e", "created_at": "2026-11-01T15:41:33Z", "updated_at": "2026-11-01T22:46:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA-mRNA pairs in cisplatin-resistant ovarian cancer.", "doi": "10.1186/s12885-021-08166-z", "pmid": "33892654", "authors": ["Bai Xue", "Shupeng Li", "Xianyu Jin", "Lifeng Liu"], "journal": "BMC cancer", "year": 2021, "abstract": "BACKGROUND: Ovarian cancer (OC) is a gynecological malignancy with the highest mortality rate. Cisplatin (DDP) based chemotherapy is a standard strategy for ovarian cancer. Despite good response rates for initial chemotherapy, almost 80% of the patients treated with DDP based chemotherapy will experience recurrence due to drug-resistant, which will ultimately result in fatality. The aim of the present study was to examine the pathogenesis and potential molecular markers of cisplatin-resistant OC by studying the differential expression of mRNAs and miRNAs between cisplatin resistant OC cell lines and normal cell lines.\nMETHODS: Two mRNA datasets (GSE58470 and GSE45553) and two miRNA sequence datasets (GSE58469 and GSE148251) were downloaded from the Gene expression omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were screened by the NetworkAnalyst. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to analyze the biological functions of DEGs. The protein-protein interaction network was constructed using STRING and Cytoscape software to identify the molecular mechanisms of key signaling pathways and cellular activities. FunRich and MiRNATip databases were used to identify the target genes of the DEMs.\nRESULTS: A total of 380 DEGs, and 5 DEMs were identified. Protein-protein interaction (PPI) network of DEGs containing 379 nodes and 1049 edges was constructed, and 4 key modules and 24 hub genes related to cisplatin-resistant OC were screened. Two hundred ninety-nine target genes of the 5 DEMs were found out. Subsequently, one of these 299 target genes (UBB) belonging to the hub genes of GSE58470 and GSE45553 was identified by MCODE and CytoHubba,which was regulated by one miRNA (mir-454).\nCONCLUSIONS: One miRNA-mRNA regulatory pairs (mir-454-UBB) was established. Taken together, our study provided evidence concerning the alteration genes involved in cisplatin-resistant OC, which will help to unravel the mechanisms underlying drug resistant.", "claims": [{"id": "claim-method", "statement": "The DEGs in cisplatin resistant OC cell lines compared with parental cell lines were determined using limma algorithm [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33892654", "locator": "sections[4] \"Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs)\" paragraph 2", "quote": "The DEGs in cisplatin resistant OC cell lines compared with parental cell lines were determined using limma algorithm [19]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33892654", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251)."}], "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:33892654"], "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:GSE148251"], "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:GSE148251"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33892654", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-021-08166-z", "sha256": "sha256:93a5917d5a7ace4673d019b520807b4f83fc98887afd9d52ded17b8b570c4102", "bytes": 37866, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-021-08166-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8063430", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE148251", "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=GSE148251", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148251", "version": null, "note": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. 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The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4458710", "GSM4458711", "GSM4458712", "GSM4458713", "GSM4458714", "GSM4458715", "GSM4458716", "GSM4458717", "GSM4458718", "GSM4458719", "GSM4458720", "GSM4458721", "GSM4458722", "GSM4458723", "GSM4458724", "GSM4458725", "GSM4458726", "GSM4458727", "GSM4458728", "GSM4458729", "GSM4458730", "GSM4458731", "GSM4458732", "GSM4458733"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "16384", "taxon": "Homo sapiens; synthetic construct", "title": "MicroRNA profiling in resistance ovarian cell lines", "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:GSE45553", "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=GSE45553", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45553", "version": null, "note": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1109168", "GSM1109169", "GSM1109170", "GSM1109171", "GSM1109172", "GSM1109173", "GSM1109174", "GSM1109175"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptional profiling of ovarian cancer spheroids reveals genes and related biological pathways associated with cisplatin resistance", "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:GSE58469", "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=GSE58469", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58469", "version": null, "note": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1412105", "GSM1412106", "GSM1412107", "GSM1412108", "GSM1412109", "GSM1412110", "GSM1412111", "GSM1412112", "GSM1412113"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "8179", "taxon": "Homo sapiens", "title": "Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (microRNAs)", "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:GSE58470", "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=GSE58470", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE58470", "version": null, "note": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1412114", "GSM1412115", "GSM1412116", "GSM1412117", "GSM1412118", "GSM1412119", "GSM1412120", "GSM1412121", "GSM1412122"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular profiling of ovarian carcinoma platinum-sensitive and -resistant cell lines (gene expression)", "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:33892654:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fe815dcff715df9de7735033017e34d2950f579b41053621174f7ed6a24019a8", "bytes": 833, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#Tab1", "version": null, "note": "24 hub genes of GSE58470 and GSE45553", "structure": {"pmcid": "PMC8063430", "section_index": 12, "section_title": "Establishment of PPI network and identification of hub gene", "row_count": 25, "column_count": 3}, "table": {"label": "Table 1", "caption": "24 hub genes of GSE58470 and GSE45553", "rows": [["Gene symbol", "Degree", "MCC Score"], ["MX1", "22", "479000000"], ["IFIT1", "17", "479000000"], ["IFIT2", "16", "479000000"], ["OASL", "28", "479000000"], ["IFIT3", "15", "479000000"], ["DDX58", "25", "479000000"], ["IFIH1", "24", "479000000"], ["DDX60", "15", "479000000"], ["IFI44", "13", "479000000"], ["IFI35", "15", "479000000"], ["IFI6", "13", "479000000"], ["IFI27", "13", "479000000"], ["IFI16", "14", "479000000"], ["PSMB8", "25", "403736"], ["UBB", "40", "403798"], ["PSMB9", "21", "403736"], ["PSMC4", "19", "403475"], ["PSMA4", "19", "403473"], ["PSMD7", "14", "403392"], ["PSMD10", "14", "403332"], ["CDK1", "34", "364936"], ["MAD2L1", "25", "364750"], ["CDC25A", "22", "364044"], ["TNF", "68", "43334"]], "row_count": 25, "column_count": 3, "numeric_cells": 56, "header_rows": 1, "locator": "section[12]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:33892654:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51939d9db31c314ab229d5d54018e5e72d12078c556657a453f0ff3788aef3f8", "bytes": 1243, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#Tab2", "version": null, "note": "GO analysis of 24 hub genes", "structure": {"pmcid": "PMC8063430", "section_index": 12, "section_title": "Establishment of PPI network and identification of hub gene", "row_count": 16, "column_count": 5}, "table": {"label": "Table 2", "caption": "GO analysis of 24 hub genes", "rows": [["Category", "ID", "Description", "Count", "P-value"], ["Molecular function", "GO:0005515", "Protein binding", "21", "< 0.001"], ["GO:0005524", "ATP binding", "6", "0.039"], ["GO:0003725", "Double-stranded RNA binding", "4", "< 0.001"], ["GO:0004298", "Threonine-type endopeptidase activity", "3", "< 0.001"], ["GO:0003727", "Single-stranded RNA binding", "3", "0.001"], ["Cellular component", "GO:0005829", "Cytosol", "19", "< 0.001"], ["GO:0005737", "Cytoplasm", "17", "< 0.001"], ["GO:0005634", "Nucleus", "14", "0.007"], ["GO:0005654", "Nucleoplasm", "10", "0.005"], ["GO:0000502", "Proteasome complex", "6", "< 0.001"], ["Biological process", "GO:0009615", "Response to virus", "10", "< 0.001"], ["GO:0060337", "Type I interferon signaling pathway", "9", "< 0.001"], ["GO:0051436", "Negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle", "9", "< 0.001"], ["GO:0051437", "Positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition", "9", "< 0.001"], ["GO:0031145", "Anaphase-promoting complex-dependent catabolic process", "9", "< 0.001"]], "row_count": 16, "column_count": 5, "numeric_cells": 45, "header_rows": 1, "locator": "section[12]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:33892654:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1b63059ac8dc75ef5dfb790f1f2639262520a90b6cb2c745883460e08d8c8331", "bytes": 697, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[3]#Tab3", "version": null, "note": "KEGG analysis of the 24 hub genes", "structure": {"pmcid": "PMC8063430", "section_index": 12, "section_title": "Establishment of PPI network and identification of hub gene", "row_count": 11, "column_count": 4}, "table": {"label": "Table 3", "caption": "KEGG analysis of the 24 hub genes", "rows": [["Term", "Description", "Count", "P-value"], ["hsa03050", "Proteasome", "5", "< 0.001"], ["hsa05168", "Herpes simplex infection", "5", "< 0.001"], ["hsa05164", "Influenza A", "4", "0.004"], ["hsa04622", "RIG-I-like receptor signaling pathway", "3", "0.007"], ["hsa04914", "Progesterone-mediated oocyte maturation", "3", "0.011"], ["hsa05169", "Epstein-Barr virus infection", "3", "0.021"], ["hsa04110", "Cell cycle", "3", "0.022"], ["hsa05162", "Measles", "3", "0.025"], ["hsa05160", "Hepatitis C", "3", "0.025"], ["hsa05161", "Hepatitis B", "3", "0.029"]], "row_count": 11, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[12]/table-wrap[3]#Tab3"}}], "gaps": ["asset:data:geo:GSE148251 not downloaded", "asset:data:geo:GSE148251 licence not read", "asset:data:geo:GSE45553 not downloaded", "asset:data:geo:GSE45553 licence not read", "asset:data:geo:GSE58469 not downloaded", "asset:data:geo:GSE58469 licence not read", "asset:data:geo:GSE58470 not downloaded", "asset:data:geo:GSE58470 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs in cisplatin resistant OC cell lines compared with parental cell lines were determined using limma algorithm [19]."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": 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{"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE58470", "GSE45553", "GSE58469", "GSE148251"], "resolved_accessions": ["GSE58470", "GSE45553", "GSE58469", "GSE148251"], "statements": ["All data generated or analyzed during this study are included in Gene expression omnibus GEO) public database. The mRNA datasets (GSE58470, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58470 and GSE45553, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45553). The miRNA datasets (GSE58469, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58469 and GSE148251, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148251)."], "basis": "The paper names GSE58470, GSE45553, GSE58469, GSE148251 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:33892654", "data:geo:GSE148251", "asset:table:pmid:33892654:1", "asset:table:pmid:33892654:2", "asset:table:pmid:33892654:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE148251"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32731, "completion_tokens": 2329, "cached_tokens": 10752}}, "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:33892654", "type": "paper", "label": "pmid:33892654"}, {"id": "source:pmid:33892654", "type": "manuscript", "label": "PMID 33892654 full text"}, {"id": "data:geo:GSE148251", "type": "dataset", "label": "GEO GSE148251"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33892654", "type": "paper", "label": "pmid:33892654"}, {"id": "source:pmid:33892654", "type": "manuscript", "label": "PMID 33892654 full text"}, {"id": "data:geo:GSE148251", "type": "dataset", "label": "GEO GSE148251"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33892654", "type": "extraction", "used": ["source:pmid:33892654"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE148251", "type": "accession_resolution", "used": ["data:geo:GSE148251"], "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:33892654", "parent_hash": "sha256:093cfc9e5f38d8cc87a55f3726950c22d202543e837b1b92b431f0f961c64e0e", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE148251 licence not read", "asset:data:geo:GSE148251 not downloaded", "asset:data:geo:GSE45553 licence not read", "asset:data:geo:GSE45553 not downloaded", "asset:data:geo:GSE58469 licence not read", "asset:data:geo:GSE58469 not downloaded", "asset:data:geo:GSE58470 licence not read", "asset:data:geo:GSE58470 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": ["Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA-mRNA pairs in cisp"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs in cisplatin resistant OC cell lines compared with parental cell lines were determined using limma algorithm [19]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}