Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30755830", "kind": "science-record", "revision": 8, "content_hash": "sha256:86ec1ea3a35dc7fc3188ddc7f2ead76c5f23fa75336c99f031140cb49127d9e7", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:43:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis.", "doi": "10.7717/peerj.6375", "pmid": "30755830", "authors": ["Xiuzhi Zhang", "Chunyan Kang", "Ningning Li", "Xiaoli Liu", "Jinzhong Zhang", "Fenglan Gao", "Liping Dai"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression.\nMETHODS: The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis.\nRESULTS: Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and UROC1) and four (SLC22A10, UROC1, CSAG3, and CSMD1) confirmed genes were correlated with HCC-A stage and grade, respectively. SPP2 had a lower trend in HCC-A tumors and was negatively correlated with HCC-A stage and grade. The SKGs each was differentially expressed between HCC-A and at least one of other HCC groups. CD5L was identified to be favorable prognostic factor for overall survival while CSMD1 unfavorable prognostic factor for disease-free survival for HCC-A patients and HCC patients in whole. Through Oncomine database, the dysregulations of the SKGs in HCC and their clinical significance were confirmed.\nCONCLUSION: The poor prognosis of HCC-A patients might be due to their later diagnosis. The SKGs, especially the four stage-correlated genes (CD5L, SLC22A10, UROC1, and SPP2) might play important roles in HCC development, especially alcohol-related HCC development and progression. CD5L might be useful for overall survival and CSMD1 for disease-free survival predication in HCC, especially alcohol-related HCC.", "claims": [{"id": "claim-method", "statement": "The DEGs (DEGs-1) between HCC-A tumors and HCC-V tumors were identified with limma (Ritchie et al., 2015) package in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30755830", "locator": "sections[6] \"Identification of DEGs-1 (DEGs between HCC-A group and other HCC groups)\" paragraph 2", "quote": "The DEGs (DEGs-1) between HCC-A tumors and HCC-V tumors were identified with limma (Ritchie et al., 2015) package in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nraw data were generated in the study. All the original data in this study weredownloaded from the public databases including TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and Oncomine (https://www.oncomine.org/).\nFor the SKGs identification, we used TCGA-LIHC (https://portal.gdc.cancer.gov/projects/TCGA-LIHC) and GSE59259 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse59259).\nThe HCC datasets from the Oncomine database (https://www.oncomine.org) were: Chen liver, Mas liver, Roessler liver, Roessler liver 2, Wurmbach liver, Jia liver, and Iizuka Liver 2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30755830", "locator": "sections[33] \"Data Availability Statement\" paragraphs 1-5", "quote": "The following information was supplied regarding data availability:\nraw data were generated in the study. All the original data in this study weredownloaded from the public databases including TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and Oncomine (https://www.oncomine.org/).\nFor the SKGs identification, we used TCGA-LIHC (https://portal.gdc.cancer.gov/projects/TCGA-LIHC) and GSE59259 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse59259).\nThe HCC datasets from the Oncomine database (https://www.oncomine.org) were: Chen liver, Mas liver, Roessler liver, Roessler liver 2, Wurmbach liver, Jia liver, and Iizuka Liver 2."}], "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:30755830"], "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:GSE59259"], "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:GSE59259"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30755830", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.6375", "sha256": "sha256:6666114fd9509aa58fcb7e5c9e974fad17f3d9cc9dfb27919e2d7a26241e93a3", "bytes": 66534, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.6375", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6368834", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE59259", "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=GSE59259", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59259", "version": null, "note": "The following information was supplied regarding data availability:\nraw data were generated in the study. All the original data in this study weredownloaded from the public databases including TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and Oncomine (https://www.oncomine.org/).\nFor the SKGs identification, we used TCGA-LIHC (https://portal.gdc.cancer.gov/projects/TCGA-LIHC) and GSE59259 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse59259).\nThe HCC datasets from the Oncomine database (https://www.oncomine.org) were: Chen liver, Mas liver, Roessler liver, Roessler liver 2, Wurmbach liver, Jia liver, and Iizuka Liver 2.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nraw data were generated in the study. All the original data in this study weredownloaded from the public databases including TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and Oncomine (https://www.oncomine.org/).\nFor the SKGs identification, we used TCGA-LIHC (https://portal.gdc.cancer.gov/projects/TCGA-LIHC) and GSE59259 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse59259).\nThe HCC datasets from the Oncomine database (https://www.oncomine.org) were: Chen liver, Mas liver, Roessler liver, Roessler liver 2, Wurmbach liver, Jia liver, and Iizuka Liver 2.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1431957", "GSM1431958", "GSM1431959", "GSM1431960", "GSM1431961", "GSM1431962", "GSM1431963", "GSM1431964", "GSM1431965", "GSM1431966", "GSM1431967", "GSM1431968", "GSM1431969", "GSM1431970", "GSM1431971", "GSM1431972"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "18451", "taxon": "Homo sapiens", "title": "Expression profiles in alcohol-associated 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": "asset:table:pmid:30755830:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d6d2ea03b1ebb3761a1d51252a1fe413ff5cfe6dbaf7adb3922d269da971b105", "bytes": 2153, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#table-1", "version": null, "note": "Clinicopathological characteristics of HCC patients# from TCGA database.", "structure": {"pmcid": "PMC6368834", "section_index": 3, "section_title": "Data processing and analysis of HCC patients from TCGA database", "row_count": 24, "column_count": 9}, "table": {"label": "Table 1", "caption": "Clinicopathological characteristics of HCC patients# from TCGA database.", "rows": [["Variable", "HCC-N (n = 91)", "HCC-A (n = 68)", "HCC-B (n = 74)", "HCC-C (n = 32)", "HCC-AB (n = 20)", "HCC-AC (n = 14)", "HCC-NAF (n = 11)", "Total (n = 310)"], ["Risk factors", "None", "Alcohol", "HBV", "HCV", "HBV alcohol", "HCV alcohol", "Non-alcoholic fatty liver disease", ""], ["Age at diagnosis (year)", "p = 0.001"], ["<60", "39(42.6%)", "23(33.8%)", "50(67.6%)", "13(40.6%)", "13(65.0%)", "6(42.9%)", "3(27.3%)", ""], ["≥60", "52(57.4%)", "45(66.2%)", "24(32.4%)", "19(59.4%)", "7(35.0%)", "8(57.1%)", "8(72.7%)", ""], ["Gender", "p = 1.305E-13"], ["Male", "32(35.2%)", "57(83.8%)", "57(77.3%)", "25(78.1%)", "20(100%)", "13(92.9%)", "5(45.5%)", ""], ["Female", "59(64.8%)", "11(16.2%)", "17(22.7%)", "7(21.9%)", "0(0%)", "1(7.1%)", "6(54.5%)", ""], ["Pathologic stage", "p = 0.010"], ["Stage I", "30(33.0%)", "20(22.0%)", "46(62.3%)", "16(50.0%)", "15(75.0%)", "9(64.3%)", "5(45.4%)", ""], ["Stage II", "20(22.3%)", "13(19.1%)", "16(21.6%)", "7(21.9%)", "3(15%)", "3(21.4%)", "3(27.3%)", ""], ["Stage III", "33(36.2%)", "25(36.8%)", "7(9.4%)", "5(15.6%)", "2(10%)", "1(7.1%)", "0(0%)", ""], ["Stage IV", "1(1.1%)", "1(1.5%)", "2(2.7%)", "0(0%)", "0(0%)", "0(0%)", "0(0%)", ""], ["NA", "7(7.7%)", "7(10.3%)", "3(4.0%)", "4(12.5%)", "0(10%)", "1(7.1%)", "3(27.3)", ""], ["Pathologic grade", "p = 0.002"], ["G1", "13(14.3%)", "10(14.7%)", "6(8.1%)", "7(21.9%)", "5(25.0%)", "4(28.6%)", "2(18.2%)", ""], ["G2", "46(50.5%)", "38(55.9%)", "27(36.5%)", "13(40.6%)", "13(65.0%)", "7(50%)", "8(72.7%)", ""], ["G3", "27(29.7%)", "19(27.9%)", "33(44.6%)", "9(28.1%)", "2(10%)", "3(21.4%)", "1(9.1%)", ""], ["G4", "1(1.1%)", "0(0%)", "7(9.4%)", "0(0%)", "0(0%)", "0(0%)", "0(0%)", ""], ["NA", "4(4.4%)", "1(1.5%)", "1(1.4%)", "3(9.4%)", "0(0%)", "0(0%)", "0(0%)", ""], ["Family history of cancer", "p = 1.598E-4"], ["None", "43(47.3%)", "45(66.2%)", "53(71.6%)", "14(43.7%)", "18(96.0%)", "7(50.0%)", "5(45.5%)", ""], ["Yes", "42(46.1%)", "12(17.6%)", "14(18.9%)", "7(21.9%)", "2(4.0%)", "6(42.9%)", "6(54.5%)", ""], ["NA", "6(6.6%)", "11(16.2%)", "7(9.5%)", "11(34.4%)", "0(0%)", "1(7.1%)", "0(0%)", ""]], "row_count": 24, "column_count": 9, "numeric_cells": 134, "header_rows": 1, "locator": "section[3]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:30755830:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1f19f7214190d2892be0cf5dc2c029c8061a4724791a343be182de76e97fd432", "bytes": 476, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#table-2", "version": null, "note": "Cox regression analysis (stepwise) of the variables# in HCC patients.", "structure": {"pmcid": "PMC6368834", "section_index": 13, "section_title": "Pathological stage determines the overall and disease-free survival of HCC patients", "row_count": 3, "column_count": 6}, "table": {"label": "Table 2", "caption": "Cox regression analysis (stepwise) of the variables# in HCC patients.", "rows": [["Survival analysis", "Prognostic factor", "B", "SE", "HR(95.0% CI)", "p"], ["Overall survival§", "Pathological stage", "0.390", "0.129", "1.477(1.147–1.902)", "0.003"], ["Disease-free survival", "Pathological stage", "0.331", "0.153", "1.392(1.031–1.880)", "0.031"]], "row_count": 3, "column_count": 6, "numeric_cells": 9, "header_rows": 1, "locator": "section[13]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:30755830:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3361a7870260458f7903202c4e049ba486548753ab6f0ee6c197e6791c83ed07", "bytes": 410, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#table-3", "version": null, "note": "Comparison of pathological stages among different HCC groups.", "structure": {"pmcid": "PMC6368834", "section_index": 14, "section_title": "HCC-A patients are diagnosed later than HCC patients with other risk factors", "row_count": 2, "column_count": 11}, "table": {"label": "Table 3", "caption": "Comparison of pathological stages among different HCC groups.", "rows": [["Group", "HCC-A", "HCC-N", "HCC-B", "HCC-C", "HCC-AB", "HCC-AC", "HCC-NAF", "Chi-Square", "DF", "p"], ["Mean rank", "168.53", "167.24", "118.45", "128.89", "104.90", "109.31", "111.00", "33.012", "6", "1.429E-5**"]], "row_count": 2, "column_count": 11, "numeric_cells": 10, "header_rows": 1, "locator": "section[14]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:30755830:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e199acdebdc152f1e93052d16b32347c7bb90dc3ed2878cfdccd67bcb99d260e", "bytes": 443, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#table-4", "version": null, "note": 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860, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[17]/table-wrap[1]#table-5", "version": null, "note": "Correlations analysis between SKGs and the pathological stage and grade of HCC-A tumors.", "structure": {"pmcid": "PMC6368834", "section_index": 17, "section_title": "SKGs identification", "row_count": 12, "column_count": 5}, "table": {"label": "Table 5", "caption": "Correlations analysis between SKGs and the pathological stage and grade of HCC-A tumors.", "rows": [["Variable", "Correlation with pathological stage (n = 61)", "Correlation with pathological grade (n = 67)"], ["R", "p value", "R", "p value"], ["SLC22A10", "−0.378", "0.003**", "−0.368", "0.002**"], ["CD5L", "−0.333", "0.009**", "−0.160", "0.196"], ["UROC1", "−0.320", "0.012*", "−0.346", "0.004**"], ["SPP2", "−0.298", "0.020*", "−0.440", "2.933E-7**"], ["CSAG3", "−0.162", "0.211", "0.289", "0.018*"], ["CSMD1", "0.083", "0.524", "0.293", "0.016*"], ["MAGEA3", "−0.062", "0.635", "0.138", "0.266"], ["IGF2", "−0.032", "0.806", "−0.151", "0.221"], ["CSAG1", "−0.025", "0.850", "0.214", "0.082"], ["MAGEA6", "−0.006", "0.963", "0.204", "0.099"]], "row_count": 12, "column_count": 5, "numeric_cells": 43, "header_rows": 2, "locator": "section[17]/table-wrap[1]#table-5"}}, {"id": "asset:table:pmid:30755830:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:434897e78e3c18f0cf85ca30c08f43ff8bc04b3165ebf07c1915b764088cb9c7", "bytes": 629, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#table-6", "version": null, "note": "Cox regression analysis# for overall survival and disease-free survival in HCC-A patients.", "structure": {"pmcid": "PMC6368834", "section_index": 18, "section_title": "Prognostic factors for overall and disease-free survival of HCC-A patients", "row_count": 5, "column_count": 7}, "table": {"label": "Table 6", "caption": "Cox regression analysis# for overall survival and disease-free survival in HCC-A patients.", "rows": [["Survival analysis", "Strata variable", "Prognostic factor", "B", "SE", "HR(95.0% CI)", "p"], ["Overall survival", "None", "CD5L", "−0.205", "0.071", "0.814(0.709–0.936)", "0.004**"], ["Pathological stage", "None", "", "", "", ""], ["Disease-free survival", "None", "CSMD1", "0.432", "0.126", "1.540(1.204–1.970)", "0.001**"], ["Pathological grade", "CSMD1", "0.315", "0.123", "1.370(1.076–1.744)", "0.021*"]], "row_count": 5, "column_count": 7, "numeric_cells": 13, "header_rows": 1, "locator": "section[18]/table-wrap[1]#table-6"}}, {"id": "asset:table:pmid:30755830:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:46c930736d4fb73ca177f5ca6b4c26d38bc4110d5a6b6475390a130cc04fe377", "bytes": 1219, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#table-7", "version": null, "note": "Expressional differences of SKGs in HCC datasets from Oncomine database.", "structure": {"pmcid": "PMC6368834", "section_index": 20, "section_title": "Validation of SKGs through Oncomine database", "row_count": 11, "column_count": 7}, "table": {"label": "Table 7", "caption": "Expressional differences of SKGs in HCC datasets from Oncomine database.", "rows": [["", "Cancer vs. normal", "Chen liver (n = 197)", "Mas liver (n = 115)", "Roessler liver (n = 43)", "Roessler liver 2 (n = 445)", "Wurmbach liver (n = 75)"], ["CD5L", "Fold change p", "− 7.2759.22E-19**", "1.0440.605", "−5.1682.51E-18**", "−5.3086.52E-95**", "−6.7001.23E-9**"], ["IGF2", "Fold change p", "−3.0801.32E-5**", "−1.7352.25E-4**", "−3.1630.015*", "−4.1543.43E-16**", "−10.1202.27E-6**"], ["UROC1", "Fold change p", "NA", "NA", "NA", "NA", "-2.1920.004**"], ["SLC22A10", "Fold change p", "NA", "NA", "NA", "NA", "NA"], ["SPP2", "Fold change p", "−4.9825.74E-15**", "2.4827.60E-5**", "−9.5813.27E-7**", "−5.7901.18E-42**", "−3.0860.006**"], ["CSMD1", "Fold change p", "1.2560.011*", "NA", "NA", "NA", "1.3140.034*"], ["CSAG1", "Fold change p", "NA", "NA", "NA", "NA", "NA"], ["CSAG3", "Fold change P", "NA", "NA", "NA", "NA", "NA"], ["MAGEA3", "Fold change p", "NA", "1.1130.139", "2.4500.011*", "2.7582.53E-17**", "2.8330.001**"], ["MAGEA6", "Fold change P", "NA", "1.1650.094", "2.4450.009**", "2.5112.16E-17**", "3.2172.73E-4**"]], "row_count": 11, "column_count": 7, "numeric_cells": 32, "header_rows": 1, "locator": "section[20]/table-wrap[1]#table-7"}}], "gaps": ["asset:data:geo:GSE59259 not downloaded", "asset:data:geo:GSE59259 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", 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"quote": "Cox regression"}}, {"id": "method-4", "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 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE59259"], "resolved_accessions": ["GSE59259"], "statements": ["The following information was supplied regarding data availability:\nraw data were generated in the study. All the original data in this study weredownloaded from the public databases including TCGA (https://portal.gdc.cancer.gov/), GEO (https://www.ncbi.nlm.nih.gov/geo/) and Oncomine (https://www.oncomine.org/).\nFor the SKGs identification, we used TCGA-LIHC (https://portal.gdc.cancer.gov/projects/TCGA-LIHC) and GSE59259 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse59259).\nThe HCC datasets from the Oncomine database (https://www.oncomine.org) were: Chen liver, Mas liver, Roessler liver, Roessler liver 2, Wurmbach liver, Jia liver, and Iizuka Liver 2."], "basis": "The paper names GSE59259 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30755830", "data:geo:GSE59259", "asset:table:pmid:30755830:1", "asset:table:pmid:30755830:2", "asset:table:pmid:30755830:3", "asset:table:pmid:30755830:4", "asset:table:pmid:30755830:5", "asset:table:pmid:30755830:6", "asset:table:pmid:30755830:7"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE59259"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 53604, "completion_tokens": 3857, "cached_tokens": 792}}, "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:30755830", "type": "paper", "label": "pmid:30755830"}, {"id": "source:pmid:30755830", "type": "manuscript", "label": "PMID 30755830 full text"}, {"id": "data:geo:GSE59259", "type": "dataset", "label": "GEO GSE59259"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30755830", "type": "paper", "label": "pmid:30755830"}, {"id": "source:pmid:30755830", "type": "manuscript", "label": "PMID 30755830 full text"}, {"id": "data:geo:GSE59259", "type": "dataset", "label": "GEO GSE59259"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30755830", "type": "extraction", "used": ["source:pmid:30755830"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE59259", "type": "accession_resolution", "used": ["data:geo:GSE59259"], "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:30755830", "parent_hash": "sha256:3cbb0a7faa6852dfc999e6488b94041800a8f44d9863156fc6a28a83ceabc0d6", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE59259 licence not read", "asset:data:geo:GSE59259 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs (DEGs-1) between HCC-A tumors and HCC-V tumors were identified with limma (Ritchie et al., 2015) package in R software."], "order_basis": "analysis_only", "id": "assay:1"}]}