{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30310500", "kind": "science-record", "revision": 8, "content_hash": "sha256:64e069b41f5398abb2c90a64a9b7cd9de27fa9083bcfb72cda1be2d96f8a8305", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A miRNA Combination as Promising Biomarker for Hepatocellular Carcinoma Diagnosis: A Study Based on Bioinformatics Analysis.", "doi": "10.7150/jca.26101", "pmid": "30310500", "authors": ["Jia Ji", "Hao Chen", "Xiao-Ping Liu", "Yu-Hui Wang", "Chang-Liang Luo", "Wu-Wen Zhang", "Wen Xie", "Fu-Bing Wang"], "journal": "Journal of Cancer", "year": 2018, "abstract": "Background: miRNAs dysregulate in hepatocellular carcinoma (HCC), showing promise for diagnostic biomarkers which may be found through exploration of differentially expressed miRNAs when comparing HCC and normal liver tissues. Materials and Methods: In the present research, candidate miRNAs were selected and verified using screening dataset GSE12717 and training dataset GSE10694, respectively. A miRNA combination was constructed using stepwise logistic regression analysis and validated using two datasets GSE74618 and TCGA. Target genes of miRNAs in the combination were obtained using a miRNA target gene prediction database. Functional analysis was conducted using an online tool DAVID. We also analyzed the mRNA-Seq data of project LIHC from TCGA to identify the hub target genes of the miRNAs. Results: A miRNA combination, which is composed of hsa-miR-221 and hsa-miR-29c was defined in this study. The miRNA combination is more effective in discriminating HCC patients from normal individuals than individual miRNAs. Additionally, the combined miRNAs showed a lower misdiagnosis rate than AFP in HCC diagnosis. In terms of the functional analysis, a total of 27 target genes of hsa-miR-221 and 96 target genes of hsa-miR-29c were obtained. Among which, INSIG1 was the common target of the two miRNAs. It was also found that both previously mentioned miRNAs played important roles in the regulation of transcription, cell proliferation, and involvement in cancer-related pathways. Lastly, 2 hub target genes of hsa-miR-221 and 16 hub target genes of hsa-miR-29c were obtained. Conclusion: We established a miRNA combination as a promising tool for HCC diagnosis, and the target genes we predicted provide possible points of penetration for researching these two miRNAs in HCC.", "claims": [{"id": "claim-method", "statement": "Spearman's rank correlation was employed to analyze the relationship between miRNAs and miRNA combinations with clinicopathological variables.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30310500", "locator": "sections[7] \"Analysis of the correlation of miRNAs and miRNA combination with clinicopathological variables\" paragraph 2", "quote": "Spearman's rank correlation was employed to analyze the relationship between miRNAs and miRNA combinations with clinicopathological variables."}], "state": "complete"}, {"id": "claim-data-access", "statement": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30310500", "locator": "sections[4] \"Dataset collection and miRNA screening\" paragraph 2", "quote": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further 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:30310500"], "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:GSE10694"], "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:GSE10694"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30310500", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.26101", "sha256": "sha256:fedd6a83faca908d15711230d96b2ef463ba27735b5b39c42c77dc000b2ce943", "bytes": 50992, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.26101", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6171011", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10694", "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=GSE10694", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10694", "version": null, "note": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM270322", "GSM270323", "GSM270324", "GSM270325", "GSM270326", "GSM270327", "GSM270328", "GSM270329", "GSM270330", "GSM270331", "GSM270332", "GSM270333", "GSM270334", "GSM270335", "GSM270336", "GSM270337", "GSM270338", "GSM270339", "GSM270340", "GSM270341", "GSM270342", "GSM270343", "GSM270344", "GSM270345", "GSM270346", "GSM270347", "GSM270348", "GSM270349", "GSM270350", "GSM270351", "GSM270352", "GSM270353", "GSM270354", "GSM270355", "GSM270356", "GSM270357", "GSM270358", "GSM270359", "GSM270360", "GSM270361", "GSM270362", "GSM270363", "GSM270364", "GSM270365", "GSM270366", "GSM270367", "GSM270368", "GSM270369", "GSM270370", "GSM270371", "GSM270372", "GSM270373", "GSM270374", "GSM270375", "GSM270376", "GSM270377", "GSM270378", "GSM270379", "GSM270380", "GSM270381", "GSM270382", "GSM270383", "GSM270384", "GSM270385", "GSM270386", "GSM270387", "GSM270388", "GSM270389", "GSM270390", "GSM270391", "GSM270392", "GSM270393", "GSM270394", "GSM270395", "GSM270396", "GSM270397", "GSM270398", "GSM270399", "GSM270400", "GSM270401", "GSM270402", "GSM270403", "GSM270404", "GSM270405", "GSM270406", "GSM270407", "GSM270408", "GSM270409", "GSM270410", "GSM270411", "GSM270412", "GSM270413", "GSM270414", "GSM270415", "GSM270416", "GSM270417", "GSM270418", "GSM270419", "GSM270420", "GSM270421", "GSM270422", "GSM270423", "GSM270424", "GSM270425", "GSM270426", "GSM270427", "GSM270428", "GSM270429", "GSM270430", "GSM270431", "GSM270432", "GSM270433", "GSM270434", "GSM270435", "GSM270436", "GSM270437", "GSM270438", "GSM270439", "GSM270440", "GSM270441", "GSM270442", "GSM270443", "GSM270444", "GSM270445", "GSM270446", "GSM270447", "GSM270448", "GSM270449", "GSM270450", "GSM270451", "GSM270452", "GSM270453", "GSM270454", "GSM270455", "GSM270456", "GSM270457", "GSM270458", "GSM270459", "GSM270460", "GSM270461", "GSM270462", "GSM270463", "GSM270464", "GSM270465", "GSM270466", "GSM270467", "GSM270468", "GSM270469", "GSM270470", "GSM270471", "GSM270472", "GSM270473", "GSM270474", "GSM270475", "GSM270476", "GSM270477", "GSM270478", "GSM270479", "GSM270480", "GSM270481", "GSM270482", "GSM270483", "GSM270484", "GSM270485", "GSM270486", "GSM270487"], "sample_count": 166, "group_sizes": null, "group_sizes_basis": null, "platform": "6542", "taxon": "Homo sapiens", "title": "MicroRNAs expression profile in human hepatocellular carcinoma", "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:GSE12717", "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=GSE12717", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12717", "version": null, "note": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM319221", "GSM319222", "GSM319223", "GSM319228", "GSM319229", "GSM319231", "GSM319234", "GSM319235", "GSM319237", "GSM319239", "GSM319241", "GSM319242", "GSM319244", "GSM319245", "GSM319247", "GSM319248"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "7274", "taxon": "Mus musculus; Homo sapiens; Rattus norvegicus", "title": "miRNA profiles of HCC from Southeast China", "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:GSE74618", "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=GSE74618", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74618", "version": null, "note": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1924292", "GSM1924293", "GSM1924294", "GSM1924295", "GSM1924296", "GSM1924297", "GSM1924298", "GSM1924299", "GSM1924300", "GSM1924301", "GSM1924302", "GSM1924303", "GSM1924304", "GSM1924305", "GSM1924306", "GSM1924307", "GSM1924308", "GSM1924309", "GSM1924310", "GSM1924311", "GSM1924312", "GSM1924313", "GSM1924314", "GSM1924315", "GSM1924316", "GSM1924317", "GSM1924318", "GSM1924319", "GSM1924320", "GSM1924321", "GSM1924322", "GSM1924323", "GSM1924324", "GSM1924325", "GSM1924326", "GSM1924327", "GSM1924328", "GSM1924329", "GSM1924330", "GSM1924331", "GSM1924332", "GSM1924333", "GSM1924334", "GSM1924335", "GSM1924336", "GSM1924337", "GSM1924338", "GSM1924339", "GSM1924340", "GSM1924341", "GSM1924342", "GSM1924343", "GSM1924344", "GSM1924345", "GSM1924346", "GSM1924347", "GSM1924348", "GSM1924349", "GSM1924350", "GSM1924351", "GSM1924352", "GSM1924353", "GSM1924354", "GSM1924355", "GSM1924356", "GSM1924357", "GSM1924358", "GSM1924359", "GSM1924360", "GSM1924361", "GSM1924362", "GSM1924363", "GSM1924364", "GSM1924365", "GSM1924366", "GSM1924367", "GSM1924368", "GSM1924369", "GSM1924370", "GSM1924371", "GSM1924372", "GSM1924373", "GSM1924374", "GSM1924375", "GSM1924376", "GSM1924377", "GSM1924378", "GSM1924379", "GSM1924380", "GSM1924381", "GSM1924382", "GSM1924383", "GSM1924384", "GSM1924385", "GSM1924386", "GSM1924387", "GSM1924388", "GSM1924389", "GSM1924390", "GSM1924391", "GSM1924392", "GSM1924393", "GSM1924394", "GSM1924395", "GSM1924396", "GSM1924397", "GSM1924398", "GSM1924399", "GSM1924400", "GSM1924401", "GSM1924402", "GSM1924403", "GSM1924404", "GSM1924405", "GSM1924406", "GSM1924407", "GSM1924408", "GSM1924409", "GSM1924410", "GSM1924411", "GSM1924412", "GSM1924413", "GSM1924414", "GSM1924415", "GSM1924416", "GSM1924417", "GSM1924418", "GSM1924419", "GSM1924420", "GSM1924421", "GSM1924422", "GSM1924423", "GSM1924424", "GSM1924425", "GSM1924426", "GSM1924427", "GSM1924428", "GSM1924429", "GSM1924430", "GSM1924431", "GSM1924432", "GSM1924433", "GSM1924434", "GSM1924435", "GSM1924436", "GSM1924437", "GSM1924438", "GSM1924439", "GSM1924440", "GSM1924441", "GSM1924442", "GSM1924443", "GSM1924444", "GSM1924445", "GSM1924446", "GSM1924447", "GSM1924448", "GSM1924449", "GSM1924450", "GSM1924451", "GSM1924452", "GSM1924453", "GSM1924454", "GSM1924455", "GSM1924456", "GSM1924457", "GSM1924458", "GSM1924459", "GSM1924460", "GSM1924461", "GSM1924462", "GSM1924463", "GSM1924464", "GSM1924465", "GSM1924466", "GSM1924467", "GSM1924468", "GSM1924469", "GSM1924470", "GSM1924471", "GSM1924472", "GSM1924473", "GSM1924474", "GSM1924475", "GSM1924476", "GSM1924477", "GSM1924478", "GSM1924479", "GSM1924480", "GSM1924481", "GSM1924482", "GSM1924483", "GSM1924484", "GSM1924485", "GSM1924486", "GSM1924487", "GSM1924488", "GSM1924489", "GSM1924490", "GSM1924491", "GSM1924492", "GSM1924493", "GSM1924494", "GSM1924495", "GSM1924496", "GSM1924497", "GSM1924498", "GSM1924499", "GSM1924500", "GSM1924501", "GSM1924502", "GSM1924503", "GSM1924504", "GSM1924505", "GSM1924506", "GSM1924507", "GSM1924508", "GSM1924509", "GSM1924510", "GSM1924511", "GSM1924512", "GSM1924513", "GSM1924514", "GSM1924515", "GSM1924516", "GSM1924517", "GSM1924518", "GSM1924519", "GSM1924520", "GSM1924521", "GSM1924522", "GSM1924523", "GSM1924524", "GSM1924525", "GSM1924526", "GSM1924527", "GSM1924528", "GSM1924529", "GSM1924530", "GSM1924531", "GSM1924532", "GSM1924533", "GSM1924534", "GSM1924535", "GSM1924536", "GSM1924537", "GSM1924538", "GSM1924539", "GSM1924540", "GSM1924541"], "sample_count": 250, "group_sizes": null, "group_sizes_basis": null, "platform": "14613", "taxon": "Homo sapiens; synthetic construct", "title": "Re-expression of fetal IGF2 as a target for hepatocellular carcinoma therapy", "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:30310500:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ccece5e4f7e6a061d685de8c9ce7b64d070d0ac7452d9cbf87af1501801ded48", "bytes": 1068, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T1", "version": null, "note": "Candidate miRNAs to establish the diagnostic combination", "structure": {"pmcid": "PMC6171011", "section_index": 12, "section_title": "DEmiRNA analysis and screening of candidate miRNAs", "row_count": 12, "column_count": 8}, "table": {"label": "Table 1", "caption": "Candidate miRNAs to establish the diagnostic combination", "rows": [["miRNA", "Screening dataset", "", "Training dataset"], ["Log FC", "P value", "type", "", "Log FC", "adj.P value", "type"], ["Hsa-miR-424", "-3.49307", "0.005137", "Down", "", "-1.63196", "3.03E-07", "Down"], ["Hsa-miR-520f", "-3.36844", "0.013892", "Down", "", "-1.19342", "8.42E-10", "Down"], ["Hsa-miR-29c", "-2.27737", "0.03304", "Down", "", "-1.84006", "2.17E-08", "Down"], ["Hsa-miR-101", "-1.82946", "0.041984", "Down", "", "-2.10304", "3.77E-09", "Down"], ["Hsa-miR-422a", "-2.61368", "0.001059", "Down", "", "-1.03471", "1.36E-09", "Down"], ["Hsa-miR-106b", "1.929812", "0.007399", "Up", "", "1.270324", "0.000267", "Up"], ["Hsa-miR-25", "1.949887", "0.001366", "Up", "", "1.690017", "2.23E-07", "Up"], ["Hsa-miR-93", "2.217326", "0.003224", "Up", "", "1.128434", "0.000155", "Up"], ["Hsa-miR-222", "2.491835", "0.000312", "Up", "", "2.385102", "1.36E-09", "Up"], ["Hsa-miR-221", "1.887786", "0.004491", "Up", "", "2.665307", "5.11E-11", "Up"]], "row_count": 12, "column_count": 8, "numeric_cells": 50, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30310500:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ba633cc9bb3a4bedd6f1991608e24712aedde5c1e77a955945e5d8bd6ed1bd22", "bytes": 991, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "Diagnostic accuracy of miRNAs and the miRNA combination", "structure": {"pmcid": "PMC6171011", "section_index": 14, "section_title": "Validating the miRNA combination using two different datasets", "row_count": 12, "column_count": 7}, "table": {"label": "Table 2", "caption": "Diagnostic accuracy of miRNAs and the miRNA combination", "rows": [["Group", "miRNA", "AUC", "P Value", "Sensitivity%", "Specificity%", "95% CI"], ["Training dataset", "hsa-miR-221", "0.9859", "<0.0001", "97.44", "100", "0.9634-1.000"], ["hsa-miR-29c", "0.9641", "<0.0001", "89.74", "100", "0.9274-1.000"], ["miRNA combination", "0.9974", "<0.0001", "98.72", "100", "0.9907-1.000"], ["", "", "", "", "", "", ""], ["Validation dataset GSE74618", "hsa-miR-221", "0.8823", "<0.0001", "75.23", "90", "0.8078-0.9569"], ["hsa-miR-29c", "0.6805", "0.05376", "61.93", "80", "0.5655-0.7955"], ["miRNA combination", "0.9092", "<0.0001", "86.7", "80", "0.8294-0.9890"], ["", "", "", "", "", "", ""], ["Validation dataset TCGA", "hsa-miR-221", "0.8473", "<0.0001", "74.13", "86", "0.8002-0.8944"], ["hsa-miR-29c", "0.9020", "<0.0001", "78.93", "90", "0.8698-0.9341"], ["miRNA combination", "0.9641", "<0.0001", "86.67", "98", "0.9474-0.9807"]], "row_count": 12, "column_count": 7, "numeric_cells": 53, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:30310500:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30c7f8b845bcb86660bab49e47771b9d6b560d03a15fa38ba07abffe1f495ed6", "bytes": 1073, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T3", "version": null, "note": "Correlation of miRNAs and miRNA combination with clinicopathological variables in HCC of TCGA datasets", "structure": {"pmcid": "PMC6171011", "section_index": 15, "section_title": "The correlation of miRNAs and the miRNA combination with HCC clinicopathological variables", "row_count": 18, "column_count": 9}, "table": {"label": "Table 3", "caption": "Correlation of miRNAs and miRNA combination with clinicopathological variables in HCC of TCGA datasets", "rows": [["", "Group", "Case", "hsa-miR-221", "hsa-miR-29c", "miRNA combination"], ["r", "p", "r", "p", "r", "p"], ["AFP", "≥20", "131", "0.189", "0.001", "-0.345", "0.00", "0.349", "0.00"], ["<20", "151"], ["Grade", "1-2", "232", "0.176", "0.001", "-0.194", "0.00", "0.238", "0.00"], ["3-4", "137"], ["TNM stage", "Ⅰ-Ⅱ", "282", "-0.036", "0.504", "-0.096", "0.073", "0.059", "0.275"], ["Ⅲ-Ⅳ", "91"], ["Tumor stage", "T0-T1", "184", "-0.056", "0.210", "-0.13", "0.02", "0.03", "0.562"], ["T2-T4", "188"], ["Lymph-node metastasis", "N0", "255", "-0.039", "0.533", "-0.0102", "0.101", "0.256", "0.071"], ["N1", "4"], ["Distant metastasis", "M0", "270", "-0.012", "0.839", "-0.003", "0.965", "-0.017", "0.785"], ["M1", "4"], ["Child-pugh", "A", "221", "0.047", "0.471", "0.027", "0.677", "0.001", "0.993"], ["B-C", "22"], ["Liver fibrosis", "Yes", "140", "0.156", "0.022", "-0.007", "0.915", "0.12", "0.077"], ["No", "76"]], "row_count": 18, "column_count": 9, "numeric_cells": 70, "header_rows": 2, "locator": "section[15]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:GSE10694 not downloaded", "asset:data:geo:GSE10694 licence not read", "asset:data:geo:GSE12717 not downloaded", "asset:data:geo:GSE12717 licence not read", "asset:data:geo:GSE74618 not downloaded", "asset:data:geo:GSE74618 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Spearman's rank correlation was employed to analyze the relationship between miRNAs and miRNA combinations with clinicopathological variables."}}, {"id": "method-2", "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-3", "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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-4", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.7, "band": "medium", "quote": "logistic regression"}}, {"id": "method-5", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}], "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": ["spearman_rho"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: spearman."}, "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": ["GSE12717", "GSE10694", "GSE74618"], "resolved_accessions": ["GSE12717", "GSE10694", "GSE74618"], "statements": ["An original microarray dataset, GSE12717 was downloaded from NCBI-Gene Expression Omnibus database (NCBI-GEO) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12717), which is based on the platform of GPL7274 CapitalBio human/mouse/rat non-coding RNA microarray. Expression of 347 miRNAs in 5 human HCC tumor samples and 3 healthy liver samples were available, of which 313 human miRNAs were selected for further analysis."], "basis": "The paper names GSE12717, GSE10694, GSE74618 in NCBI-Gene Expression Omnibus database (NCBI-GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["spearman_rho"], "assets": ["source:pmid:30310500", "data:geo:GSE10694", "asset:table:pmid:30310500:1", "asset:table:pmid:30310500:2", "asset:table:pmid:30310500:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10694"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 41137, "completion_tokens": 2802, "cached_tokens": 784}}, "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:30310500", "type": "paper", "label": "pmid:30310500"}, {"id": "source:pmid:30310500", "type": "manuscript", "label": "PMID 30310500 full text"}, {"id": "data:geo:GSE10694", "type": "dataset", "label": "GEO GSE10694"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30310500", "type": "paper", "label": "pmid:30310500"}, {"id": "source:pmid:30310500", "type": "manuscript", "label": "PMID 30310500 full text"}, {"id": "data:geo:GSE10694", "type": "dataset", "label": "GEO GSE10694"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30310500", "type": "extraction", "used": ["source:pmid:30310500"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10694", "type": "accession_resolution", "used": ["data:geo:GSE10694"], "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:30310500", "parent_hash": "sha256:e3b8a8901d258b1a033aa2954f7a772925d3f579dd8374bdb57ae45fa20a5b27", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE10694 licence not read", "asset:data:geo:GSE10694 not downloaded", "asset:data:geo:GSE12717 licence not read", "asset:data:geo:GSE12717 not downloaded", "asset:data:geo:GSE74618 licence not read", "asset:data:geo:GSE74618 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": "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 of microarray data were analyzed using R package “limma”,"], "order_basis": "paper_text_order:3381", "id": "assay:1"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Spearman's rank correlation was employed to analyze the relationship between miRNAs and miRNA combinations with clinicopathological variables."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:52:37+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}