Identification of the Sixth Complement Component as Potential Key Genes in Hepatocellular Carcinoma via Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33083480", "kind": "science-record", "revision": 7, "content_hash": "sha256:2b97455e3640e0efb3206e30bd2c61425c75ce118ff7057fedf1fe6271e2e3fb", "created_at": "2026-11-01T15:41:13Z", "updated_at": "2026-11-01T22:02:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the Sixth Complement Component as Potential Key Genes in Hepatocellular Carcinoma via Bioinformatics Analysis.", "doi": "10.1155/2020/7042124", "pmid": "33083480", "authors": ["Di Mu", "Feng Qin", "Baoshan Li", "Qian Zhou"], "journal": "BioMed research international", "year": 2020, "abstract": "The present study is designed to determine potential target genes involved in hepatocellular carcinoma (HCC) and provide possible underlying mechanisms of action. Several studies (GSE112790, GSE87630, and GSE56140) from the GEO database looking at molecular characteristics in HCC were screened and analyzed by GEO2R, which led to the identification of a total of 93 differentially expressed genes (DEGs). From the protein-protein interaction (PPI) network, we selected 13 key genes with high degree of variability in expression in HCC. Expression of three key genes (NQO1, CYP2C9, and C6) presented with poor overall survival (OS) in HCC patients by UALCAN. C6, which is a complement component, was found by ONCOMINE and TIMER to have low expression in many solid cancers including HCC. Besides, Kaplan-Meier plotter and UALCAN database analysis to access diseases prognosis suggested that low expression of C6 is significantly related to worse OS in LIHC patients, especially in advanced HCC patients. Finally, the TIMER analysis suggested that the C6 expression showed significant negative correlation with infiltrating levels of six immune cells. The somatic copy number alterations (SCNAs) of C6 were associated with CD4+ T cell infiltration in HCC. Taken together, these results together identified C6 as a potential key gene in the diagnosis and prognosis of HCC.", "claims": [{"id": "claim-method", "statement": "DEGs between the HCC groups and the nontumor groups in the three datasets were determined by the online tool GEO2R, using following cutoff criteria: adjusted P value should be less than 0.01, and the absolute value of log FC (fold change) should be above 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33083480", "locator": "sections[3] \"2.1. Microarray Data and Identification of DEGs\" paragraph 3", "quote": "DEGs between the HCC groups and the nontumor groups in the three datasets were determined by the online tool GEO2R, using following cutoff criteria: adjusted P value should be less than 0.01, and the absolute value of log FC (fold change) should be above 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33083480", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33083480"], "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:GSE112790"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE112790"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33083480", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2020/7042124", "sha256": "sha256:479c9463dc9bb6df079d9ae1f64632391df8efa26656479e61e1cd59607961f1", "bytes": 38141, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2020/7042124", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7556077", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"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 open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "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:GSE56140", "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=GSE56140", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE56140", "version": null, "note": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1356496", "GSM1356497", "GSM1356498", "GSM1356499", "GSM1356500", "GSM1356501", "GSM1356502", "GSM1356503", "GSM1356504", "GSM1356505", "GSM1356506", "GSM1356507", "GSM1356508", "GSM1356509", "GSM1356510", "GSM1356511", "GSM1356512", "GSM1356513", "GSM1356514", "GSM1356515", "GSM1356516", "GSM1356517", "GSM1356518", "GSM1356519", "GSM1356520", "GSM1356521", "GSM1356522", "GSM1356523", "GSM1356524", "GSM1356525", "GSM1356526", "GSM1356527", "GSM1356528", "GSM1356529", "GSM1356530", "GSM1356531", "GSM1356532", "GSM1356533", "GSM1356534", "GSM1356535", "GSM1356536", "GSM1356537", "GSM1356538", "GSM1356539", "GSM1356540", "GSM1356541", "GSM1356542", "GSM1356543", "GSM1356544", "GSM1356545", "GSM1356546", "GSM1356547", "GSM1356548", "GSM1356549", "GSM1356550", "GSM1356551", "GSM1356552", "GSM1356553", "GSM1356554", "GSM1356555", "GSM1356556", "GSM1356557", "GSM1356558", "GSM1356559", "GSM1356560", "GSM1356561", "GSM1356562", "GSM1356563", "GSM1356564"], "sample_count": 69, "group_sizes": null, "group_sizes_basis": null, "platform": "18461", "taxon": "Homo sapiens", "title": "Heterogeneity of gene-expression profiles of hepatocellular carcinoma tumors", "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:GSE87630", "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=GSE87630", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87630", "version": null, "note": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2335922", "GSM2335923", "GSM2335924", "GSM2335925", "GSM2335926", "GSM2335927", "GSM2335928", "GSM2335929", "GSM2335930", "GSM2335931", "GSM2335932", "GSM2335933", "GSM2335934", "GSM2335935", "GSM2335936", "GSM2335937", "GSM2335938", "GSM2335939", "GSM2335940", "GSM2335941", "GSM2335942", "GSM2335943", "GSM2335944", "GSM2335945", "GSM2335946", "GSM2335947", "GSM2335948", "GSM2335949", "GSM2335950", "GSM2335951", "GSM2335952", "GSM2335953", "GSM2335954", "GSM2335955", "GSM2335956", "GSM2335957", "GSM2335958", "GSM2335959", "GSM2335960", "GSM2335961", "GSM2335962", "GSM2335963", "GSM2335964", "GSM2335965", "GSM2335966", "GSM2335967", "GSM2335968", "GSM2335969", "GSM2335970", "GSM2335971", "GSM2335972", "GSM2335973", "GSM2335974", "GSM2335975", "GSM2335976", "GSM2335977", "GSM2335978", "GSM2335979", "GSM2335980", "GSM2335981", "GSM2335982", "GSM2335983", "GSM2335984", "GSM2335985", "GSM2335986", "GSM2335987", "GSM2335988", "GSM2335989", "GSM2335990", "GSM2335991", "GSM2335992", "GSM2335993", "GSM2335994", "GSM2335995", "GSM2335996", "GSM2335997", "GSM2335998", "GSM2335999", "GSM2336000", "GSM2336001", "GSM2336002", "GSM2336003", "GSM2336004", "GSM2336005", "GSM2336006", "GSM2336007", "GSM2336008", "GSM2336009", "GSM2336010", "GSM2336011", "GSM2336012", "GSM2336013", "GSM2336014", "GSM2336015"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Integrated analysis of genomic and epigenomic regulation of transcriptome identifies molecular subtypes of liver cancer (gene expression)", "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:33083480:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b4995d9c16d0e3346770f18c7fce019bb7aded4e5705bb9f6449b027a49b5476", "bytes": 366, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab1", "version": null, "note": "Characteristics of the three datasets.", "structure": {"pmcid": "PMC7556077", "section_index": 12, "section_title": "3.1. Identification, Function Enrichment Analysis of DEGs, and Selection of Key Genes", "row_count": 4, "column_count": 4}, "table": {"label": "Table 1", "caption": "Characteristics of the three datasets.", "rows": [["Dataset ID", "Country", "Number of samples", "Platform"], ["GSE112790", "Japan", "183T 15N", "GPL570"], ["GSE87630", "Korea", "64T 30N", "GPL6947"], ["GSE56140", "USA", "35T 34N", "GPL18461"]], "row_count": 4, "column_count": 4, "numeric_cells": 9, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:33083480:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4e3042ae372a74aef87ec2a5331378d4f0c96a5f2b7662ed78fd3f3a783eb920", "bytes": 539, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab2", "version": null, "note": "The correlation of the C6 mRNA expression and overall survival in other four cancer types with UALCAN database.", "structure": {"pmcid": "PMC7556077", "section_index": 14, "section_title": "3.3. The C6 Expression Level and Prognostic Potential across Various Cancer", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "The correlation of the C6 mRNA expression and overall survival in other four cancer types with UALCAN database.", "rows": [["Cancer types", "C6 mRNA expression", "Overall survival"], ["", "Expression level∗", "P value", "P value"], ["BRCA", "Downregulation", "1.50E-05", "0.15"], ["COAD", "Downregulation", "1.55E-02", "0.9"], ["HNSC", "Downregulation", "1.66E-03", "0.77"], ["LUSC", "Downregulation", "6.41E-07", "0.21"]], "row_count": 6, "column_count": 4, "numeric_cells": 8, "header_rows": 2, "locator": "section[14]/table-wrap[1]#tab2"}}], "gaps": ["asset:data:geo:GSE112790 not downloaded", "asset:data:geo:GSE112790 licence not read", "asset:data:geo:GSE56140 not downloaded", "asset:data:geo:GSE56140 licence not read", "asset:data:geo:GSE87630 not downloaded", "asset:data:geo:GSE87630 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"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": "GO enrichment"}}, {"id": "method-5", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEGs between the HCC groups and the nontumor groups in the three datasets were determined by the online tool GEO2R, using following cutoff criteria: adjusted P value should be less than 0.01, and the absolute value of log FC (fold change) should be above 1.5."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE112790", "GSE87630", "GSE56140"], "resolved_accessions": ["GSE112790", "GSE87630", "GSE56140"], "statements": ["The open available data sources or tools are as following: (1) http://www.ncbi.nlm.nih.gov/geo/, (2) http://bioinformatics.psb.ugent.be/webtools/Venn/, (3) https://david.ncifcrf.gov/, (4) http://gepia.cancer-pku.cn/index.html, (5) https://www.oncomine.org/resource/login.html, (6) https://cistrome.shinyapps.io/timer/, and (7) http://ualcan.path.uab.edu/."], "basis": "The paper names GSE112790, GSE87630, GSE56140 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": [], "assets": ["source:pmid:33083480", "data:geo:GSE112790", "asset:table:pmid:33083480:1", "asset:table:pmid:33083480:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE112790"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31718, "completion_tokens": 2534, "cached_tokens": 10504}}, "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:33083480", "type": "paper", "label": "pmid:33083480"}, {"id": "source:pmid:33083480", "type": "manuscript", "label": "PMID 33083480 full text"}, {"id": "data:geo:GSE112790", "type": "dataset", "label": "GEO GSE112790"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33083480", "type": "paper", "label": "pmid:33083480"}, {"id": "source:pmid:33083480", "type": "manuscript", "label": "PMID 33083480 full text"}, {"id": "data:geo:GSE112790", "type": "dataset", "label": "GEO GSE112790"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33083480", "type": "extraction", "used": ["source:pmid:33083480"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE112790", "type": "accession_resolution", "used": ["data:geo:GSE112790"], "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:33083480", "parent_hash": "sha256:809249e1c50a4c9ea8dbe0d51a24967301e55a221fcd71165b6ca05023463837", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE112790 licence not read", "asset:data:geo:GSE112790 not downloaded", "asset:data:geo:GSE56140 licence not read", "asset:data:geo:GSE56140 not downloaded", "asset:data:geo:GSE87630 licence not read", "asset:data:geo:GSE87630 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"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": ["Hepatitis, Chongqing Medical University. HCC cell lines were cultured in DMEM (Hyclone) medium supplemented with 1", "qing Medical University. HCC cell lines were cultured in DMEM (Hyclone) medium supplemented with 1% p"], "order_basis": "paper_text_order:3376", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}