Up-Regulation of hsa-miR-210 Promotes Venous Metastasis and Predicts Poor Prognosis in Hepatocellular Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30560088", "kind": "science-record", "revision": 9, "content_hash": "sha256:bc15a5cf38c8f118e11c0f4fd47e1594b9111be52404609b20dd61e3ae80edc6", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T22:43:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Up-Regulation of hsa-miR-210 Promotes Venous Metastasis and Predicts Poor Prognosis in Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2018.00569", "pmid": "30560088", "authors": ["Jia Ji", "Yuan Rong", "Chang-Liang Luo", "Shuo Li", "Xiang Jiang", "Hong Weng", "Hao Chen", "Wu-Wen Zhang", "Wen Xie", "Fu-Bing Wang"], "journal": "Frontiers in oncology", "year": 2018, "abstract": "Objective: To investigate the potential biomarkers for venous metastasis of hepatocellular carcinoma (HCC), and briefly discuss their target genes and the signaling pathways they are involved in. Materials and Method: The dataset GSE6857 was downloaded from GEO. Significantly differentially expressed miRNAs were identified using the R package \"limma,\" After that, the survival analysis was conducted to discover the significance of these up-regulated miRNAs for the prognosis of HCC patients. Additionally, miRNAs which were up-regulated in venous metastasis positive HCC tissues and were significant for the prognosis of HCC patients were further verified in clinical samples using RT-qPCR. The miRNAs were then analyzed for their correlations with clinical characteristics including survival time, AFP level, pathological grade, TNM stage, tumor stage, lymph-node metastasis, distant metastasis, child-pugh score, vascular invasion, liver fibrosis and race using 375 HCC samples downloaded from the TCGA database. The target genes of these miRNAs were obtained using a miRNA target gene prediction database, and their functions were analyzed using the online tool DAVID. Results: 15 miRNAs were differentially expressed in samples with venous metastasis, among which 7 were up-regulated in venous metastasis positive HCC samples. As one of the up-regulated miRNAs, hsa-miR-210 was identified as an independent prognostic factor for HCC. Using RT-qPCR, it was evident that hsa-miR-210 expression was significantly higher in venous metastasis positive HCC samples (p = 0.0036). Further analysis indicated that hsa-miR-210 was positively associated with AFP level, pathological grade, TNM stage, tumor stage and vascular invasion. A total of 168 hsa-miR-210 target genes, which are mainly related to tumor metastasis and tumor signaling pathways, were also predicted in this study. Conclusion: hsa-miR-210 might promote vascular invasion of HCC cells and could be used as a prognostic biomarker.", "claims": [{"id": "claim-method", "statement": "Kaplan-Meier survival analysis was conducted for univariate survival analysis, while Cox proportional hazards regression analysis was used for multivariate survival analysis (the analysis method is Forward:LR). The high throughput miRNA data of 375 HCC tissues and corresponding donors' information were downloaded from TCGA (https://cancergenome.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30560088", "locator": "sections[12] \"Statistical analysis\" paragraph 3", "quote": "Kaplan-Meier survival analysis was conducted for univariate survival analysis, while Cox proportional hazards regression analysis was used for multivariate survival analysis (the analysis method is Forward:LR)."}, {"asset": "source:pmid:30560088", "locator": "sections[5] \"Screening of prognostic miRNAs\" paragraph 2", "quote": "The high throughput miRNA data of 375 HCC tissues and corresponding donors' information were downloaded from TCGA (https://cancergenome.nih.gov/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Primary data and platform annotation file of dataset GSE6857 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6857) were downloaded from GEO. The platform of this dataset is OSU-CCC MicroRNA Microarray Version 2.0 (GPL4700) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4700). The dataset contains the expression profile of 230 miRNAs in 240 paired HCC tissues and adjacent non-tumor liver tissues, 1 lymph node tissue sample of an HCC patient and 1 normal liver tissue. In this study, we chose 180 HCC tissues without venous metastasis and 60 HCC tissues with venous metastasis to conduct the analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30560088", "locator": "sections[4] \"Screening of venous metastasis-related miRNAs\" paragraph 2", "quote": "Primary data and platform annotation file of dataset GSE6857 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6857) were downloaded from GEO. The platform of this dataset is OSU-CCC MicroRNA Microarray Version 2.0 (GPL4700) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4700). The dataset contains the expression profile of 230 miRNAs in 240 paired HCC tissues and adjacent non-tumor liver tissues, 1 lymph node tissue sample of an HCC patient and 1 normal liver tissue. In this study, we chose 180 HCC tissues without venous metastasis and 60 HCC tissues with venous metastasis to conduct the analysis."}], "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:30560088"], "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:GSE6857"], "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:GSE6857"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30560088", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2018.00569", "sha256": "sha256:3cde0f2004c747839162823c13d1623eed766fe47dd1843dc227c2cb6b714d65", "bytes": 40937, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2018.00569", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6287006", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE6857", "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=GSE6857", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6857", "version": null, "note": "Primary data and platform annotation file of dataset GSE6857 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6857) were downloaded from GEO. The platform of this dataset is OSU-CCC MicroRNA Microarray Version 2.0 (GPL4700) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4700). The dataset contains the expression profile of 230 miRNAs in 240 paired HCC tissues and adjacent non-tumor liver tissues, 1 lymph node tissue sample of an HCC patient and 1 normal liver tissue. In this study, we chose 180 HCC tissues without venous metastasis and 60 HCC tissues with venous metastasis to conduct the analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Primary data and platform annotation file of dataset GSE6857 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6857) were downloaded from GEO. The platform of this dataset is OSU-CCC MicroRNA Microarray Version 2.0 (GPL4700) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4700). The dataset contains the expression profile of 230 miRNAs in 240 paired HCC tissues and adjacent non-tumor liver tissues, 1 lymph node tissue sample of an HCC patient and 1 normal liver tissue. In this study, we chose 180 HCC tissues without venous metastasis and 60 HCC tissues with venous metastasis to conduct the analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM157887", "GSM157888", "GSM157889", "GSM157890", "GSM157891", "GSM157892", "GSM157893", "GSM157894", "GSM157895", "GSM157896", "GSM157897", "GSM157898", "GSM157899", "GSM157900", "GSM157901", "GSM157902", "GSM157903", "GSM157904", "GSM157905", "GSM157906", "GSM157907", "GSM157908", "GSM157909", "GSM157910", "GSM157911", "GSM157912", "GSM157913", "GSM157914", "GSM157915", "GSM157916", "GSM157917", "GSM157918", "GSM157919", "GSM157920", "GSM157921", "GSM157922", "GSM157923", "GSM157924", "GSM157925", "GSM157926", "GSM157927", "GSM157928", "GSM157929", "GSM157930", "GSM157931", "GSM157932", "GSM157933", "GSM157934", "GSM157935", "GSM157936", "GSM157937", "GSM157938", "GSM157939", "GSM157940", "GSM157941", "GSM157942", "GSM157943", "GSM157944", "GSM157945", "GSM157946", "GSM157947", "GSM157948", "GSM157949", "GSM157950", "GSM157951", "GSM157952", "GSM157953", "GSM157954", "GSM157955", "GSM157956", "GSM157957", "GSM157958", "GSM157959", "GSM157960", "GSM157961", "GSM157962", "GSM157963", "GSM157964", "GSM157965", "GSM157966", "GSM157967", "GSM157968", "GSM157969", "GSM157970", "GSM157971", "GSM157972", "GSM157973", "GSM157974", "GSM157975", "GSM157976", "GSM157977", "GSM157978", "GSM157979", "GSM157980", "GSM157981", "GSM157982", "GSM157983", "GSM157984", "GSM157985", "GSM157986", "GSM157987", "GSM157988", "GSM157989", "GSM157990", "GSM157991", "GSM157992", "GSM157993", "GSM157994", "GSM157995", "GSM157996", "GSM157997", "GSM157998", "GSM157999", "GSM158000", "GSM158001", "GSM158002", "GSM158003", "GSM158004", "GSM158005", "GSM158006", "GSM158007", "GSM158008", "GSM158009", "GSM158010", "GSM158011", "GSM158012", "GSM158013", "GSM158014", "GSM158015", "GSM158016", "GSM158017", "GSM158018", "GSM158019", "GSM158020", "GSM158021", "GSM158022", "GSM158023", "GSM158024", "GSM158025", "GSM158026", "GSM158027", "GSM158028", "GSM158029", "GSM158030", "GSM158031", "GSM158032", "GSM158033", "GSM158034", "GSM158035", "GSM158036", "GSM158037", "GSM158038", "GSM158039", "GSM158040", "GSM158041", "GSM158042", "GSM158043", "GSM158044", "GSM158045", "GSM158046", "GSM158047", "GSM158048", "GSM158049", "GSM158050", "GSM158051", "GSM158052", "GSM158053", "GSM158054", "GSM158055", "GSM158056", "GSM158057", "GSM158058", "GSM158059", "GSM158060", "GSM158061", "GSM158062", "GSM158063", "GSM158064", "GSM158065", "GSM158066", "GSM158067", "GSM158068", "GSM158069", "GSM158070", "GSM158071", "GSM158072", "GSM158073", "GSM158074", "GSM158075", "GSM158076", "GSM158077", "GSM158078", "GSM158079", "GSM158080", "GSM158081", "GSM158082", "GSM158083", "GSM158084", "GSM158085", "GSM158086", "GSM158087", "GSM158088", "GSM158089", "GSM158090", "GSM158091", "GSM158092", "GSM158093", "GSM158094", "GSM158095", "GSM158096", "GSM158097", "GSM158098", "GSM158099", "GSM158100", "GSM158101", "GSM158102", "GSM158103", "GSM158104", "GSM158105", "GSM158106", "GSM158107", "GSM158108", "GSM158109", "GSM158110", "GSM158111", "GSM158112", "GSM158113", "GSM158114", "GSM158115", "GSM158116", "GSM158117", "GSM158118", "GSM158119", "GSM158120", "GSM158121", "GSM158122", "GSM158123", "GSM158124", "GSM158125", "GSM158126", "GSM158127", "GSM337903", "GSM337904", "GSM337905", "GSM337906", "GSM337907", "GSM337908", "GSM337909", "GSM337910", "GSM337911", "GSM337912", "GSM337913", "GSM337914", "GSM337915", "GSM337916", "GSM337917", "GSM337918", "GSM337919", "GSM337920", "GSM337921", "GSM337922", "GSM337923", "GSM337924", "GSM337925", "GSM337926", "GSM337927", "GSM337928", "GSM337929", "GSM337930", "GSM337931", "GSM337932", "GSM337933", "GSM337934", "GSM337935", "GSM337936", "GSM337937", "GSM337938", "GSM337939", "GSM337940", "GSM337941", "GSM337942", "GSM337943", "GSM337944", "GSM337945", "GSM337946", "GSM337947", "GSM337948", "GSM337949", "GSM337950", "GSM337951", "GSM337952", "GSM337953", "GSM337954", "GSM337955", "GSM337956", "GSM337957", "GSM337958", "GSM337959", "GSM337960", "GSM337961", "GSM337962", "GSM337963", "GSM337964", "GSM337965", "GSM337966", "GSM337967", "GSM337968", "GSM337969", "GSM337970", "GSM337971", "GSM337972", "GSM337973", "GSM337974", "GSM337975", "GSM337976", "GSM337977", "GSM337978", "GSM337979", "GSM337980", "GSM337981", "GSM337982", "GSM337983", "GSM337984", "GSM337985", "GSM337986", "GSM337987", "GSM337988", "GSM337989", "GSM337990", "GSM337991", "GSM337992", "GSM337993", "GSM337994", "GSM337995", "GSM337996", "GSM337997", "GSM337998", "GSM337999", "GSM338000", "GSM338001", "GSM338002", "GSM338003", "GSM338004", "GSM338005", "GSM338006", "GSM338007", "GSM338008", "GSM338009", "GSM338010", "GSM338011", "GSM338012", "GSM338013", "GSM338014", "GSM338015", "GSM338016", "GSM338017", "GSM338018", "GSM338019", "GSM338020", "GSM338021", "GSM338022", "GSM338023", "GSM338024", "GSM338025", "GSM338026", "GSM338027", "GSM338028", "GSM338029", "GSM338030", "GSM338031", "GSM338032", "GSM338033", "GSM338034", "GSM338035", "GSM338036", "GSM338037", "GSM338038", "GSM338039", "GSM338040", "GSM338041", "GSM338042", "GSM338043", "GSM338044", "GSM338045", "GSM338046", "GSM338047", "GSM338048", "GSM338049", "GSM338050", "GSM338051", "GSM338052", "GSM338053", "GSM338054", "GSM338055", "GSM338056", "GSM338057", "GSM338058", "GSM338059", "GSM338060", "GSM338061", "GSM338062", "GSM338063", "GSM338064", "GSM338065", "GSM338066", "GSM338067", "GSM338068", "GSM338069", "GSM338070", "GSM338071", "GSM338072", "GSM338073", "GSM338074", "GSM338075", "GSM338076", "GSM338077", "GSM338078", "GSM338079", "GSM338080", "GSM338081", "GSM338082", "GSM338083", "GSM338084", "GSM338085", "GSM338086", "GSM338087", "GSM338088", "GSM338089", "GSM338090", "GSM338091", "GSM338092", "GSM338093", "GSM338094", "GSM338095", "GSM338096", "GSM338097", "GSM338098", "GSM338099", "GSM338100", "GSM338101", "GSM338102", "GSM338103", "GSM338104", "GSM338105", "GSM338106", "GSM338107", "GSM338108", "GSM338109", "GSM338110", "GSM338111", "GSM338112", "GSM338113", "GSM338114", "GSM338115", "GSM338116", "GSM338117", "GSM338118", "GSM338119", "GSM338120", "GSM338121", "GSM338122", "GSM338123", "GSM338124", "GSM338125", "GSM338126", "GSM338127", "GSM338128", "GSM338129", "GSM338130", "GSM338131", "GSM338132", "GSM338133", "GSM338134", "GSM338135", "GSM338136", "GSM338137", "GSM338138", "GSM338139", "GSM338140", "GSM338141", "GSM338142", "GSM338143"], "sample_count": 482, "group_sizes": null, "group_sizes_basis": null, "platform": "4700", "taxon": "Mus musculus; Homo sapiens", "title": "Unique MicroRNA Expression Signature Predicts Survival, Metastases and Recurrence of HCC", "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:30560088:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27a4f55077399244fa5276da717570070247c3ba8d347486c8df33d12ef375fd", "bytes": 990, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T1", "version": null, "note": "Significantly differentially expressed miRNAs in venous metastasis positive HCC tissues.", "structure": {"pmcid": "PMC6287006", "section_index": 14, "section_title": "Venous metastasis-related miRNAs in HCC", "row_count": 17, "column_count": 4}, "table": {"label": "Table 1", "caption": "Significantly differentially expressed miRNAs in venous metastasis positive HCC tissues.", "rows": [["miRNA", "Screening dataset"], ["", "Log FC", "Adj P-value", "Type"], ["hsa-miR-301", "0.842786", "0.000267078", "Up"], ["hsa-let-7e", "0.847988", "9.04E-11", "Up"], ["hsa-let-7b", "0.850236", "2.94E-12", "Up"], ["hsa-miR-31", "0.853136", "5.34E-07", "Up"], ["hsa-miR-210", "0.868472", "1.68E-06", "Up"], ["hsa-miR-371", "0.991324", "1.92E-10", "Up"], ["hsa-miR-183", "1.027867", "1.14E-05", "Up"], ["hsa-miR-367", "−1.08021", "1.81E-06", "Down"], ["hsa-miR-22", "−0.9947", "0.00055601", "Down"], ["hsa-miR-182", "−0.94816", "0.00023209", "Down"], ["hsa-miR-100", "−0.94307", "9.38E-07", "Down"], ["hsa-miR-1b-1", "−0.87813", "0.00015521", "Down"], ["hsa-miR-101", "−0.84328", "0.000209509", "Down"], ["hsa-miR-124a-1", "−0.81885", "2.27E-08", "Down"], ["hsa-miR-101", "−0.80452", "9.15E-10", "Down"]], "row_count": 17, "column_count": 4, "numeric_cells": 45, "header_rows": 2, "locator": "section[14]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30560088:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7d9a58c1e5b80c503782c51123f3baae18ce40c7c926f2793d1adddec915266d", "bytes": 1031, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T2", "version": null, "note": "Univariate analysis of factors affecting overall survival of HCC patients.", "structure": {"pmcid": "PMC6287006", "section_index": 16, "section_title": "hsa-miR-210 is an independent prognostic factor for HCC", "row_count": 32, "column_count": 4}, "table": {"label": "Table 2", "caption": "Univariate analysis of factors affecting overall survival of HCC patients.", "rows": [["Variable", "Group", "Case number", "P"], ["Age", "< 50", "71", "0.173"], ["", "≥50", "301", ""], ["Gender", "Male", "253", "0.309"], ["", "Female", "119", ""], ["AFP", "< 20", "150", "0.019"], ["", "≥20", "130", ""], ["Grade", "1", "55", "0.858"], ["", "2", "176", ""], ["", "3", "123", ""], ["", "4", "13", ""], ["TNM stage", "I", "173", "0.000"], ["", "II", "85", ""], ["", "III", "85", ""], ["", "IV", "5", ""], ["Tumor stage", "T1", "183", "0.000"], ["", "T2", "93", ""], ["", "T3", "80", ""], ["", "T4", "13", ""], ["Lymph-node metastasis", "N0", "254", "0.317"], ["", "N1", "4", ""], ["Distant metastasis", "M0", "269", "0.01"], ["", "M1", "4", ""], ["Child-pugh", "A", "219", "0.357"], ["", "B", "21", ""], ["", "C", "1", ""], ["Liver fibrosis", "No", "75", "0.316"], ["", "Yes", "139", ""], ["Vascular invasion", "No", "206", "0.162"], ["", "Yes", "110", ""], ["Race", "Asian", "160", "0.129"], ["", "Others", "202", ""]], "row_count": 32, "column_count": 4, "numeric_cells": 51, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:30560088:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4c6cfa8d2c4f99ed56e5af4f5408dfeabab6549c08faea4e4d027169360b4bcf", "bytes": 426, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T3", "version": null, "note": "Cox proportional hazards regression analysis of factors affecting overall survival of HCC patients.", "structure": {"pmcid": "PMC6287006", "section_index": 16, "section_title": "hsa-miR-210 is an independent prognostic factor for HCC", "row_count": 3, "column_count": 6}, "table": {"label": "Table 3", "caption": "Cox proportional hazards regression analysis of factors affecting overall survival of HCC patients.", "rows": [["Variable", "B", "SE", "Sig.", "HR", "95% CI"], ["hsa-miR-210", "0.966", "0.280", "0.001", "2.627", "1.516–4.551"], ["Distant metastasis", "1.638", "0.602", "0.007", "5.146", "1.580–16.760"]], "row_count": 3, "column_count": 6, "numeric_cells": 12, "header_rows": 1, "locator": "section[16]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:30560088:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:710b61b2ca216960d736bbcf1c14f9b1bf14a9e7d31e4d5efe05a4e4d9dfe21d", "bytes": 1100, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#T4", "version": null, "note": "The relationship between hsa-mir-210 and the clinicopathological variables of HCC.", "structure": {"pmcid": "PMC6287006", "section_index": 18, "section_title": "The correlation of hsa-miR-210 with HCC clinicopathological variables", "row_count": 26, "column_count": 5}, "table": {"label": "Table 4", "caption": "The relationship between hsa-mir-210 and the clinicopathological variables of HCC.", "rows": [["", "Group", "Case", "hsa-miR-210"], ["", "", "", "R", "p"], ["Age", "< 50", "71", "0.072", "0.164"], ["", "≥50", "300", "", ""], ["Gender", "Male", "253", "0.093", "0.074"], ["", "Female", "119", "", ""], ["AFP", "< 20", "150", "0.095", "0.112"], ["", "≥20", "131", "", ""], ["Grade", "1", "55", "0.144", "0.006"], ["", "2–4", "313", "", ""], ["TNM stage", "I–II", "258", "0.197", "0.00"], ["", "III–IV", "90", "", ""], ["Tumor stage", "T0–T1", "182", "0.162", "0.002"], ["", "T2–T4", "187", "", ""], ["Lymph-node metastasis", "N0", "254", "0.061", "0.332"], ["", "N1", "4", "", ""], ["Distant metastasis", "M0", "269", "−0.005", "0.934"], ["", "M1", "4", "", ""], ["Child-pugh", "A", "220", "0.028", "0.67"], ["", "B–C", "22", "", ""], ["Liver fibrosis", "No", "75", "−0.087", "0.206"], ["", "Yes", "140", "", ""], ["Vascular invasion", "No", "206", "0.135", "0.016"], ["", "Yes", "111", "", ""], ["Race", "Asian", "160", "−0.024", "0.647"], ["", "Others", "202", "", ""]], "row_count": 26, "column_count": 5, "numeric_cells": 55, "header_rows": 2, "locator": "section[18]/table-wrap[1]#T4"}}], "gaps": ["asset:data:geo:GSE6857 not downloaded", "asset:data:geo:GSE6857 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "reordered", "quote": "Kaplan-Meier survival analysis was conducted for univariate survival analysis, while Cox proportional hazards regression analysis was used for multivariate survival analysis (the analysis method is Forward:LR). The high throughput miRNA data of 375 HCC tissues and corresponding donors' information were downloaded from TCGA (https://cancergenome.nih.gov/)."}}, {"id": "method-2", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student's t-test"}}, {"id": "method-3", "family": "group_comparison", "specific": "mann_whitney", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_mann_whitney"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Mann Whitney"}}, {"id": "method-4", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-5", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-6", "family": "differential_expression", "specific": "edger", "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": 0.8, "band": "high", "quote": "edgeR"}}, {"id": "method-7", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-8", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman's rank correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE6857"], "resolved_accessions": ["GSE6857"], "statements": ["Primary data and platform annotation file of dataset GSE6857 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6857) were downloaded from GEO. The platform of this dataset is OSU-CCC MicroRNA Microarray Version 2.0 (GPL4700) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4700). The dataset contains the expression profile of 230 miRNAs in 240 paired HCC tissues and adjacent non-tumor liver tissues, 1 lymph node tissue sample of an HCC patient and 1 normal liver tissue. In this study, we chose 180 HCC tissues without venous metastasis and 60 HCC tissues with venous metastasis to conduct the analysis."], "basis": "The paper names GSE6857 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:30560088", "data:geo:GSE6857", "asset:table:pmid:30560088:1", "asset:table:pmid:30560088:2", "asset:table:pmid:30560088:3", "asset:table:pmid:30560088:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE6857"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:26Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 33948, "completion_tokens": 2012, "cached_tokens": 11272}}, "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:30560088", "type": "paper", "label": "pmid:30560088"}, {"id": "source:pmid:30560088", "type": "manuscript", "label": "PMID 30560088 full text"}, {"id": "data:geo:GSE6857", "type": "dataset", "label": "GEO GSE6857"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30560088", "type": "paper", "label": "pmid:30560088"}, {"id": "source:pmid:30560088", "type": "manuscript", "label": "PMID 30560088 full text"}, {"id": "data:geo:GSE6857", "type": "dataset", "label": "GEO GSE6857"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30560088", "type": "extraction", "used": ["source:pmid:30560088"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE6857", "type": "accession_resolution", "used": ["data:geo:GSE6857"], "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:30560088", "parent_hash": "sha256:71a96160ef952bc5ef198f1f0314f79650a168b895573ec7c45daabb64e4510c", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE6857 licence not read", "asset:data:geo:GSE6857 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e further verified in clinical samples using RT-qPCR. The miRNAs were then analyzed for their cor", "independent prognostic factor for HCC. Using RT-qPCR, it was evident that hsa-miR-210 expression", "urther verified in clinical samples using RT-qPCR. The miRNAs were then analyzed for their cor", "ependent prognostic factor for HCC. Using RT-qPCR, it was evident that hsa-miR-210 expression"], "order_basis": "paper_text_order:753", "id": "assay:1"}, {"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": ["nificantly differentially expressed genes in microarray data were analyzed using R package “limma,”"], "order_basis": "paper_text_order:4031", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan-Meier survival analysis was conducted for univariate survival analysis, while Cox proportional hazards regression analysis was used for multivariate survival analysis (the analysis method is Forward:LR). The high throughput miRNA data of 375 HCC tissues and corresponding donors' information were downloaded from TCGA (https://cancergenome.nih.gov/)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}