Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33665036", "kind": "science-record", "revision": 8, "content_hash": "sha256:d3a5b8564bf2e7dbd4f6849b41d24e80f0f59d817af6299e0971dd145a19cf52", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T22:46:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments.", "doi": "10.7717/peerj.10943", "pmid": "33665036", "authors": ["Jie Fu", "Xiao Zhang", "Likun Yan", "Yaoli Shao", "Xinxu Liu", "Yuan Chu", "Ge Xu", "Xundi Xu"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers and the fourth leading cause of cancer-related deaths in the world. Although the treatment of HCC has made great progress in recent years, the therapeutic effects on HCC are still unsatisfactory due to difficulty in early diagnosis, chemoresistance and high recurrence rate post-surgery.\nMETHODS: In this study, we identified differentially expressed genes (DEGs) based on four Gene Expression Omnibus (GEO) datasets (GSE45267, GSE98383, GSE101685 and GSE112790) between HCC and normal hepatic tissues. A protein-protein interaction (PPI) network was established to identify the central nodes associated with HCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the central nodes were conducted to find the hub genes. The expression levels of the hub genes were validated based on the ONCOMINE and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Additionally, the genetic alterations of the hub genes were evaluated by cBioPortal. The role of the hub genes on the overall survival (OS) and relapse survival (RFS) of HCC patients was evaluated by Kaplan-Meier plotter. At last, the mechanistic role of the hub genes was illustrated by in vitro experiments.\nRESULTS: We found the following seven hub genes: BUB1B, CCNB1, CCNB2, CDC20, CDK1, MAD2L1 and RRM2 using integrated bioinformatics analysis. All of the hub genes were significantly upregulated in HCC tissues. And the seven hub genes were associated with the OS and RFS of HCC patients. Finally, in vitro experiments indicated that BUB1B played roles in HCC cell proliferation, migration, invasion, apoptosis and cell cycle by partially affecting mitochondrial functions.\nCONCLUSIONS: In summary, we identified seven hub genes that were associated with the expression and prognosis of HCC. The mechanistic oncogenic role of BUB1B in HCC was first illustrated. BUB1B might play an important role in HCC and could be potential therapeutic targets for HCC.", "claims": [{"id": "claim-method", "statement": "Student’s t-test was used in the two-group comparisons, and one-way ANOVA was used for more than two groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33665036", "locator": "sections[18] \"Statistical analysis\" paragraph 2", "quote": "Student’s t-test was used in the two-group comparisons, and one-way ANOVA was used for more than two groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33665036", "locator": "sections[32] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files."}], "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:33665036"], "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:GSE101685"], "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:GSE101685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33665036", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10943", "sha256": "sha256:993dc01c1c085df0bfb5f81c94067d9fdf75e90ecbe3b29006a84362d85e7339", "bytes": 34193, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.10943", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7908873", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101685", "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=GSE101685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101685", "version": null, "note": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2711996", "GSM2711997", "GSM2711998", "GSM2711999", "GSM2712000", "GSM2712001", "GSM2712002", "GSM2712003", "GSM2712004", "GSM2712005", "GSM2712006", "GSM2712007", "GSM2712008", "GSM2712009", "GSM2712010", "GSM2712011", "GSM2712012", "GSM2712013", "GSM2712014", "GSM2712015", "GSM2712016", "GSM2712017", "GSM2712018", "GSM2712019", "GSM2712020", "GSM2712021", "GSM2712022", "GSM2712023", "GSM2712024", "GSM2712025", "GSM2712026", "GSM2712027"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profile of hepatocellular carcinoma patients in Taiwan", "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:GSE112790", "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=GSE112790", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112790", "version": null, "note": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3083512", "GSM3083513", "GSM3083514", "GSM3083515", "GSM3083516", "GSM3083517", "GSM3083518", "GSM3083519", "GSM3083520", "GSM3083521", "GSM3083522", "GSM3083523", "GSM3083524", "GSM3083525", "GSM3083526", "GSM3083527", "GSM3083528", "GSM3083529", "GSM3083530", "GSM3083531", "GSM3083532", "GSM3083533", "GSM3083534", "GSM3083535", "GSM3083536", "GSM3083537", "GSM3083538", "GSM3083539", "GSM3083540", "GSM3083541", "GSM3083542", "GSM3083543", "GSM3083544", "GSM3083545", "GSM3083546", "GSM3083547", "GSM3083548", "GSM3083549", "GSM3083550", "GSM3083551", "GSM3083552", "GSM3083553", "GSM3083554", "GSM3083555", "GSM3083556", "GSM3083557", "GSM3083558", "GSM3083559", "GSM3083560", "GSM3083561", "GSM3083562", "GSM3083563", "GSM3083564", "GSM3083565", "GSM3083566", "GSM3083567", "GSM3083568", "GSM3083569", "GSM3083570", "GSM3083571", "GSM3083572", "GSM3083573", "GSM3083574", "GSM3083575", "GSM3083576", "GSM3083577", "GSM3083578", "GSM3083579", "GSM3083580", "GSM3083581", "GSM3083582", "GSM3083583", "GSM3083584", "GSM3083585", "GSM3083586", "GSM3083587", "GSM3083588", "GSM3083589", "GSM3083590", "GSM3083591", "GSM3083592", "GSM3083593", "GSM3083594", "GSM3083595", "GSM3083596", "GSM3083597", "GSM3083598", "GSM3083599", "GSM3083600", "GSM3083601", "GSM3083602", "GSM3083603", "GSM3083604", "GSM3083605", "GSM3083606", "GSM3083607", "GSM3083608", "GSM3083609", "GSM3083610", "GSM3083611", "GSM3083612", "GSM3083613", "GSM3083614", "GSM3083615", "GSM3083616", "GSM3083617", "GSM3083618", "GSM3083619", "GSM3083620", "GSM3083621", "GSM3083622", "GSM3083623", "GSM3083624", "GSM3083625", "GSM3083626", "GSM3083627", "GSM3083628", "GSM3083629", "GSM3083630", "GSM3083631", "GSM3083632", "GSM3083633", "GSM3083634", "GSM3083635", "GSM3083636", "GSM3083637", "GSM3083638", "GSM3083639", "GSM3083640", "GSM3083641", "GSM3083642", "GSM3083643", "GSM3083644", "GSM3083645", "GSM3083646", "GSM3083647", "GSM3083648", "GSM3083649", "GSM3083650", "GSM3083651", "GSM3083652", "GSM3083653", "GSM3083654", "GSM3083655", "GSM3083656", "GSM3083657", "GSM3083658", "GSM3083659", "GSM3083660", "GSM3083661", "GSM3083662", "GSM3083663", "GSM3083664", "GSM3083665", "GSM3083666", "GSM3083667", "GSM3083668", "GSM3083669", "GSM3083670", "GSM3083671", "GSM3083672", "GSM3083673", "GSM3083674", "GSM3083675", "GSM3083676", "GSM3083677", "GSM3083678", "GSM3083679", "GSM3083680", "GSM3083681", "GSM3083682", "GSM3083683", "GSM3083684", "GSM3083685", "GSM3083686", "GSM3083687", "GSM3083688", "GSM3083689", "GSM3083690", "GSM3083691", "GSM3083692", "GSM3083693", "GSM3083694", "GSM3083695", "GSM3083696", "GSM3083697", "GSM3083698", "GSM3083699", "GSM3083700", "GSM3083701", "GSM3083702", "GSM3083703", "GSM3083704", "GSM3083705", "GSM3083706", "GSM3083707", "GSM3083708", "GSM3083709"], "sample_count": 198, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence [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:GSE45267", "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=GSE45267", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45267", "version": null, "note": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1100370", "GSM1100371", "GSM1100372", "GSM1100373", "GSM1100374", "GSM1100375", "GSM1100376", "GSM1100377", "GSM1100378", "GSM1100379", "GSM1100380", "GSM1100381", "GSM1100382", "GSM1100383", "GSM1100384", "GSM1100385", "GSM1100386", "GSM1100387", "GSM1100388", "GSM1100389", "GSM1100390", "GSM1100391", "GSM1100392", "GSM1100393", "GSM1100394", "GSM1100395", "GSM1100396", "GSM1100397", "GSM1100398", "GSM1100399", "GSM1100400", "GSM1100401", "GSM1100402", "GSM1100403", "GSM1100404", "GSM1100405", "GSM1100406", "GSM1100407", "GSM1100408", "GSM1100409", "GSM1100410", "GSM1100411", "GSM1100412", "GSM1100413", "GSM1100414", "GSM1100415", "GSM1100416", "GSM1100417", "GSM1100418", "GSM1100419", "GSM1100420", "GSM1100421", "GSM1100422", "GSM1100423", "GSM1100424", "GSM1100425", "GSM1100426", "GSM1100427", "GSM1100428", "GSM1100429", "GSM1100430", "GSM1100431", "GSM1100432", "GSM1100433", "GSM1100434", "GSM1100435", "GSM1100436", "GSM1100437", "GSM1100438", "GSM1100439", "GSM1100440", "GSM1100441", "GSM1100442", "GSM1100443", "GSM1100444", "GSM1100445", "GSM1100446", "GSM1100447", "GSM1100448", "GSM1100449", "GSM1100450", "GSM1100451", "GSM1100452", "GSM1100453", "GSM1100454", "GSM1100455", "GSM1100456"], "sample_count": 87, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiles of human hepatocellular carcinoma (training set 1)", "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:GSE98383", "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=GSE98383", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98383", "version": null, "note": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2593011", "GSM2593012", "GSM2593013", "GSM2593014", "GSM2593015", "GSM2593016", "GSM2593017", "GSM2593018", "GSM2593019", "GSM2593020", "GSM2593021", "GSM2593022", "GSM2593023", "GSM2593024", "GSM2593025", "GSM2593026", "GSM2593027", "GSM2593028", "GSM2593029", "GSM2593030", "GSM2593031", "GSM2593032", "GSM2593033", "GSM2593034", "GSM2593035", "GSM2593036", "GSM2593037", "GSM2593038", "GSM2593039", "GSM2593040", "GSM2593041", "GSM2593042", "GSM2593043", "GSM2593044", "GSM2593045", "GSM2593046", "GSM2593047", "GSM2593048", "GSM2593049", "GSM2593050", "GSM2593051", "GSM2593052", "GSM2593053", "GSM2593054", "GSM2593055", "GSM2593056", "GSM2593057", "GSM2593058", "GSM2593059", "GSM2593060", "GSM2593061", "GSM2593062", "GSM2593063", "GSM2593064", "GSM2593065", "GSM2593066", "GSM2593067", "GSM2593068", "GSM2593069", "GSM2593070", "GSM2593071", "GSM2593072", "GSM2593073", "GSM2593074", "GSM2593075", "GSM2593076", "GSM2593077", "GSM2593078", "GSM2593079", "GSM2593080", "GSM2593081", "GSM2593082", "GSM2593083", "GSM2593084"], "sample_count": 74, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Molecular Signature of Hepatitis D Virus-Associated Hepatocellular Carcinoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33665036:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4ecffe888ee20f216a55e7d3c42fd89b83b2dc5d38d3ec3ffd6d100bc336d119", "bytes": 359, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#table-1", "version": null, "note": "Eighty-one common differentially expressed genes (DEGs) were detected from four GEO datasets, including 36 upregulated genes and 45 downregulated genes in the HCC tissues compared to normal hepatic tissues.", "structure": {"pmcid": "PMC7908873", "section_index": 20, "section_title": "Identification of DEGs in HCC", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Eighty-one common differentially expressed genes (DEGs) were detected from four GEO datasets, including 36 upregulated genes and 45 downregulated genes in the HCC tissues compared to normal hepatic tissues.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[20]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33665036:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f29f5d648fb46d5206dc058327a6c869bfe00d274c3c5f5d76101f2f62503acd", "bytes": 191, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[1]#table-2", "version": null, "note": "Gene Ontology analysis of DEGs in HCC.", "structure": {"pmcid": "PMC7908873", "section_index": 21, "section_title": "GO annotation and KEGG pathway analysis of DEGs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Gene Ontology analysis of DEGs in HCC.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[21]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:33665036:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ad78fe6781f4bfc3708a3349beeb60436298948b788d5f5a91ffc9d702a2346", "bytes": 190, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[21]/table-wrap[2]#table-3", "version": null, "note": "KEGG pathway analysis of DEGs in HCC.", "structure": {"pmcid": "PMC7908873", "section_index": 21, "section_title": "GO annotation and KEGG pathway analysis of DEGs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "KEGG pathway analysis of DEGs in HCC.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[21]/table-wrap[2]#table-3"}}, {"id": "asset:table:pmid:33665036:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:db83b4b9fa2c98bf1055f56b23993a99e56395c0e032217bd82cc35d5ab777a7", "bytes": 228, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#table-4", "version": null, "note": "Reanalysis of the 29 genes in the central nodes by KEGG pathway enrichment.", "structure": {"pmcid": "PMC7908873", "section_index": 23, "section_title": "Validation of the expression levels of the 7 Hub genes in HCC", "row_count": 0, "column_count": 0}, "table": {"label": "Table 4", "caption": "Reanalysis of the 29 genes in the central nodes by KEGG pathway enrichment.", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[23]/table-wrap[1]#table-4"}}], "gaps": ["asset:data:geo:GSE101685 not downloaded", "asset:data:geo:GSE101685 licence not read", "asset:data:geo:GSE112790 not downloaded", "asset:data:geo:GSE112790 licence not read", "asset:data:geo:GSE45267 not downloaded", "asset:data:geo:GSE45267 licence not read", "asset:data:geo:GSE98383 not downloaded", "asset:data:geo:GSE98383 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": "Student’s t-test was used in the two-group comparisons, and one-way ANOVA was used for more than two groups."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "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": "protein-protein interaction"}}, {"id": "method-4", "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"}}], "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": ["GSE45267", "GSE98383", "GSE101685", "GSE112790"], "resolved_accessions": ["GSE45267", "GSE98383", "GSE101685", "GSE112790"], "statements": ["The following information was supplied regarding data availability:Sequences are available at NCBI GEO: GSE45267, GSE98383, GSE101685 and GSE112790.Raw data are available in the Supplemental Files."], "basis": "The paper names GSE45267, GSE98383, GSE101685, GSE112790 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:33665036", "data:geo:GSE101685", "asset:table:pmid:33665036:1", "asset:table:pmid:33665036:2", "asset:table:pmid:33665036:3", "asset:table:pmid:33665036:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101685"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:33Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 27509, "completion_tokens": 1829, "cached_tokens": 656}}, "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:33665036", "type": "paper", "label": "pmid:33665036"}, {"id": "source:pmid:33665036", "type": "manuscript", "label": "PMID 33665036 full text"}, {"id": "data:geo:GSE101685", "type": "dataset", "label": "GEO GSE101685"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33665036", "type": "paper", "label": "pmid:33665036"}, {"id": "source:pmid:33665036", "type": "manuscript", "label": "PMID 33665036 full text"}, {"id": "data:geo:GSE101685", "type": "dataset", "label": "GEO GSE101685"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33665036", "type": "extraction", "used": ["source:pmid:33665036"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101685", "type": "accession_resolution", "used": ["data:geo:GSE101685"], "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:33665036", "parent_hash": "sha256:978a0c95111086b993133fd2fc7fdcd146fb572e209731ebbfa24a70a6e770ab", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE101685 licence not read", "asset:data:geo:GSE101685 not downloaded", "asset:data:geo:GSE112790 licence not read", "asset:data:geo:GSE112790 not downloaded", "asset:data:geo:GSE45267 licence not read", "asset:data:geo:GSE45267 not downloaded", "asset:data:geo:GSE98383 licence not read", "asset:data:geo:GSE98383 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["HCC cell proliferation, migration, invasion, apoptosis and cell cycle by partially affecting mitoch"], "order_basis": "paper_text_order:1768", "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": ["gh the cBioPortal database. Cell culture and transfection The human HCC cell lines HepG2 and Huh7 and", "ng (Shanghai, China). SiRNA and plasmid were transfected into HCC cells with Lipofectamine 2000 Reage", "pression plasmid and small interfering RNAs (siRNA) targeting BUB1B were purchased from ShenGon", "e purchased from ShenGong (Shanghai, China). SiRNA and plasmid were transfected into HCC cells"], "order_basis": "paper_text_order:2940", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e Academy of Sciences (Shanghai, China). All cell lines were maintained in Dulbecco’s modified Eagle medium (Gibco,", "re and transfection The human HCC cell lines HepG2 and Huh7 and the normal hepatic cell line LO"], "order_basis": "paper_text_order:2978", "id": "assay:3"}, {"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": ["Student’s t-test was used in the two-group comparisons, and one-way ANOVA was used for more than two groups."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}