← All .science files
pmid:33824863
Development and Validation of a Metabolic Gene-Based Prognostic Signature for Hepatocellular Carcinoma.
Jialei Weng · Chenhao Zhou · Qiang Zhou · Wanyong Chen · Yirui Yin · Manar Atyah · Qiongzhu Dong · Yi Shi · Ning Ren
Journal of hepatocellular carcinoma · 2021 doi:10.2147/JHC.S300633
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 9 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 488 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 37 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 5 items
[32] array · 5 items
[33] array · 5 items
[34] array · 5 items
[35] array · 5 items
[36] array · 5 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 3 items
[1] array · 3 items
[2] array · 3 items
[3] array · 3 items
[4] array · 3 items
[5] array · 3 items
[6] array · 3 items
[7] array · 3 items
[8] array · 3 items
[9] array · 3 items
[10] array · 3 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 3 items
[1] array · 2 items
[2] array · 4 items
[3] array · 3 items
[4] array · 3 items
[5] array · 4 items
[6] array · 3 items
[7] array · 3 items
[8] array · 4 items
[9] array · 3 items
[10] array · 3 items
[11] array · 4 items
[12] array · 3 items
[13] array · 3 items
[14] array · 4 items
[15] array · 3 items
[16] array · 3 items
[17] array · 4 items
[18] array · 3 items
[19] array · 3 items
[20] array · 4 items
[21] array · 3 items
[22] array · 3 items
gaps array · 2 items
analysis object · 4 fields
methods array · 5 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 6 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 2 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 5 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 6 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33824863", "kind": "science-record", "revision": 8, "content_hash": "sha256:4600672d9aaeca75f150104109c5ad695a20ad9f2a2d498b13b3b7d34128f3dd", "created_at": "2026-11-01T15:41:31Z", "updated_at": "2026-11-01T22:03:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and Validation of a Metabolic Gene-Based Prognostic Signature for Hepatocellular Carcinoma.", "doi": "10.2147/JHC.S300633", "pmid": "33824863", "authors": ["Jialei Weng", "Chenhao Zhou", "Qiang Zhou", "Wanyong Chen", "Yirui Yin", "Manar Atyah", "Qiongzhu Dong", "Yi Shi", "Ning Ren"], "journal": "Journal of hepatocellular carcinoma", "year": 2021, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is a malignant tumor with great variation in prognosis among individuals. Changes in metabolism influence disease progression and clinical outcomes. The objective of this study was to determine the overall survival (OS) risk of HCC patients from a metabolic perspective.\nPATIENTS AND METHODS: The model was constructed using the least absolute shrinkage and selection operator (LASSO) COX regression based on The Cancer Genome Atlas (TCGA, n=342) dataset. The International Cancer Genome Consortium (ICGC, n=232), GSE14520 (n=242) datasets, and a clinical cohort (n=64) were then used to assess the prognostic value of the signature.\nRESULTS: A 10 metabolic gene-based signature was constructed and verified as a robust and independent prognostic classifier in public and real-world validation cohorts. Meanwhile, the signature enabled the identification of HCC molecular subtypes, yielding an AUC value of 0.678 [95% CI: 0.592-0.763]. Besides, the signature was associated with metabolic processes like glycolysis, supported by a clear correlation between the risk score and expression of rate-limiting enzymes. Furthermore, high-risk tumor was likely to have a high tumor infiltration status of immunosuppressive cells, as well as elevated expression of some immune checkpoint molecules. For final clinical translation, a nomogram integrating the signature and tumor stage was established, and showed improved predictive accuracy of 3- and 5-year OS and brought more net benefit to patients.\nCONCLUSION: We developed a prognostic signature based on 10 metabolic genes, which has proven to be an independent and reliable prognostic predictor for HCC and reflects the metabolic and immune characteristics of tumors.", "claims": [{"id": "claim-method", "statement": "The least absolute shrinkage and selection operator (LASSO) COX regression analysis was then conducted to construct the prognostic signature with 1000-fold cross-validation using the “glmnet” package in R software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33824863", "locator": "sections[6] \"Construction of the Prognostic Metabolic-Related Gene Signature\" paragraph 2", "quote": "The least absolute shrinkage and selection operator (LASSO) COX regression analysis was then conducted to construct the prognostic signature with 1000-fold cross-validation using the “glmnet” package in R software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression and clinical information of TCGA cohort were acquired from Genomic Data Commons Data Portal and cBioPortal for Cancer Genomics, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33824863", "locator": "sections[3] \"Data Collection\" paragraph 2", "quote": "Gene expression and clinical information of TCGA cohort were acquired from Genomic Data Commons Data Portal and cBioPortal for Cancer Genomics, respectively."}], "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:33824863"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33824863", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JHC.S300633", "sha256": "sha256:ec4a4ef5d7d1f229d62b4f2c6e1b293e67b3539e6595c6fa29ce0da6a153854d", "bytes": 46139, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JHC.S300633", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8018394", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "Gene expression and clinical information of TCGA cohort were acquired from Genomic Data Commons Data Portal and cBioPortal for Cancer Genomics, respectively.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression and clinical information of TCGA cohort were acquired from Genomic Data Commons Data Portal and cBioPortal for Cancer Genomics, respectively.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM362947", "GSM362948", "GSM362949", "GSM362950", "GSM362951", "GSM362952", "GSM362953", "GSM362954", "GSM362955", "GSM362956", "GSM362957", "GSM362958", "GSM362959", "GSM362960", "GSM362961", "GSM362962", "GSM362963", "GSM362964", "GSM362965", "GSM362966", "GSM362967", "GSM362968", "GSM362969", "GSM362970", "GSM362971", "GSM362972", "GSM362973", "GSM362974", "GSM362975", "GSM362976", "GSM362977", "GSM362978", "GSM362979", "GSM362980", "GSM362981", "GSM362982", "GSM362983", "GSM362984", "GSM362985", "GSM362986", "GSM362987", "GSM362988", "GSM362989", "GSM362990", "GSM362991", "GSM362992", "GSM362993", "GSM362994", "GSM362995", "GSM362996", "GSM362997", "GSM362998", "GSM362999", "GSM363000", "GSM363001", "GSM363002", "GSM363003", "GSM363004", "GSM363005", "GSM363006", "GSM363007", "GSM363008", "GSM363009", "GSM363010", "GSM363011", "GSM363012", "GSM363013", "GSM363014", "GSM363015", "GSM363016", "GSM363017", "GSM363018", "GSM363019", "GSM363020", "GSM363021", "GSM363022", "GSM363023", "GSM363024", "GSM363025", "GSM363026", "GSM363027", "GSM363028", "GSM363029", "GSM363030", "GSM363031", "GSM363032", "GSM363033", "GSM363034", "GSM363035", "GSM363036", "GSM363037", "GSM363038", "GSM363039", "GSM363040", "GSM363041", "GSM363042", "GSM363043", "GSM363044", "GSM363045", "GSM363046", "GSM363047", "GSM363048", "GSM363049", "GSM363050", "GSM363051", "GSM363052", "GSM363053", "GSM363054", "GSM363055", "GSM363056", "GSM363057", "GSM363058", "GSM363059", "GSM363060", "GSM363061", "GSM363062", "GSM363063", "GSM363064", "GSM363065", "GSM363066", "GSM363067", "GSM363068", "GSM363069", "GSM363070", "GSM363071", "GSM363072", "GSM363073", "GSM363074", "GSM363075", "GSM363076", "GSM363077", "GSM363078", "GSM363079", "GSM363080", "GSM363081", "GSM363082", "GSM363083", "GSM363084", "GSM363085", "GSM363086", "GSM363087", "GSM363088", "GSM363089", "GSM363090", "GSM363091", "GSM363092", "GSM363093", "GSM363094", "GSM363095", "GSM363096", "GSM363097", "GSM363098", "GSM363099", "GSM363100", "GSM363101", "GSM363102", "GSM363103", "GSM363104", "GSM363105", "GSM363106", "GSM363107", "GSM363108", "GSM363109", "GSM363110", "GSM363111", "GSM363112", "GSM363113", "GSM363114", "GSM363115", "GSM363116", "GSM363117", "GSM363118", "GSM363119", "GSM363120", "GSM363121", "GSM363122", "GSM363123", "GSM363124", "GSM363125", "GSM363126", "GSM363127", "GSM363128", "GSM363129", "GSM363130", "GSM363131", "GSM363132", "GSM363133", "GSM363134", "GSM363135", "GSM363136", "GSM363137", "GSM363138", "GSM363139", "GSM363140", "GSM363141", "GSM363142", "GSM363143", "GSM363144", "GSM363145", "GSM363146", "GSM363147", "GSM363148", "GSM363149", "GSM363150", "GSM363151", "GSM363152", "GSM363153", "GSM363154", "GSM363155", "GSM363156", "GSM363157", "GSM363158", "GSM363159", "GSM363160", "GSM363161", "GSM363162", "GSM363163", "GSM363164", "GSM363165", "GSM363166", "GSM363167", "GSM363168", "GSM363169", "GSM363170", "GSM363171", "GSM363172", "GSM363173", "GSM363174", "GSM363175", "GSM363176", "GSM363177", "GSM363178", "GSM363179", "GSM363180", "GSM363181", "GSM363182", "GSM363183", "GSM363184", "GSM363185", "GSM363186", "GSM363187", "GSM363188", "GSM363189", "GSM363190", "GSM363191", "GSM363192", "GSM363193", "GSM363194", "GSM363195", "GSM363196", "GSM363197", "GSM363198", "GSM363199", "GSM363200", "GSM363201", "GSM363202", "GSM363203", "GSM363204", "GSM363205", "GSM363206", "GSM363207", "GSM363208", "GSM363209", "GSM363210", "GSM363211", "GSM363212", "GSM363213", "GSM363214", "GSM363215", "GSM363216", "GSM363217", "GSM363218", "GSM363219", "GSM363220", "GSM363221", "GSM363222", "GSM363223", "GSM363224", "GSM363225", "GSM363226", "GSM363227", "GSM363228", "GSM363229", "GSM363230", "GSM363231", "GSM363232", "GSM363233", "GSM363234", "GSM363235", "GSM363236", "GSM363237", "GSM363238", "GSM363239", "GSM363240", "GSM363241", "GSM363242", "GSM363243", "GSM363244", "GSM363245", "GSM363246", "GSM363247", "GSM363248", "GSM363249", "GSM363250", "GSM363251", "GSM363252", "GSM363253", "GSM363254", "GSM363255", "GSM363256", "GSM363257", "GSM363258", "GSM363259", "GSM363260", "GSM363261", "GSM363262", "GSM363263", "GSM363264", "GSM363265", "GSM363266", "GSM363267", "GSM363268", "GSM363269", "GSM363270", "GSM363271", "GSM363272", "GSM363273", "GSM363274", "GSM363275", "GSM363276", "GSM363277", "GSM363278", "GSM363279", "GSM363280", "GSM363281", "GSM363282", "GSM363283", "GSM363284", "GSM363285", "GSM363286", "GSM363287", "GSM363288", "GSM363289", "GSM363290", "GSM363291", "GSM363292", "GSM363293", "GSM363294", "GSM363295", "GSM363296", "GSM363297", "GSM363298", "GSM363299", "GSM363300", "GSM363301", "GSM363302", "GSM363303", "GSM363304", "GSM363305", "GSM363306", "GSM363307", "GSM363308", "GSM363309", "GSM363310", "GSM363311", "GSM363312", "GSM363313", "GSM363314", "GSM363315", "GSM363316", "GSM363317", "GSM363318", "GSM363319", "GSM363320", "GSM363321", "GSM363322", "GSM363323", "GSM363324", "GSM363325", "GSM363326", "GSM363327", "GSM363328", "GSM363329", "GSM363330", "GSM363331", "GSM363332", "GSM363333", "GSM363334", "GSM363335", "GSM363336", "GSM363337", "GSM363338", "GSM363339", "GSM363340", "GSM363341", "GSM363342", "GSM363343", "GSM363344", "GSM363345", "GSM363346", "GSM363347", "GSM363348", "GSM363349", "GSM363350", "GSM363351", "GSM363352", "GSM363353", "GSM363354", "GSM363355", "GSM363356", "GSM363357", "GSM363358", "GSM363359", "GSM363360", "GSM363361", "GSM363362", "GSM363363", "GSM363364", "GSM363365", "GSM363366", "GSM363367", "GSM363368", "GSM363369", "GSM363370", "GSM363371", "GSM363372", "GSM363373", "GSM363374", "GSM363375", "GSM363376", "GSM363378", "GSM363380", "GSM363381", "GSM363382", "GSM363384", "GSM363386", "GSM363388", "GSM363391", "GSM363393", "GSM363397", "GSM363400", "GSM363402", "GSM363404", "GSM363407", "GSM363417", "GSM363420", "GSM363421", "GSM363422", "GSM363423", "GSM363424", "GSM363425", "GSM363426", "GSM363427", "GSM363428", "GSM363429", "GSM363430", "GSM363431", "GSM363432", "GSM363433", "GSM363434", "GSM363435", "GSM363436", "GSM363437", "GSM363438", "GSM363439", "GSM363440", "GSM363441", "GSM363442", "GSM363443", "GSM363444", "GSM363445", "GSM363446", "GSM363447", "GSM363448", "GSM363449", "GSM363450", "GSM363451", "GSM712532", "GSM712533", "GSM712534", "GSM712535", "GSM712536", "GSM712537", "GSM712538", "GSM712539", "GSM712540", "GSM712541", "GSM712542"], "sample_count": 488, "group_sizes": null, "group_sizes_basis": null, "platform": "3921;571", "taxon": "Homo sapiens", "title": "Gene expression data of human hepatocellular carcinoma (HCC)", "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:33824863:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a60744a6fbd77a596f3639813e119d6ed9c3eee1a2bba75f77c60bf7f111f649", "bytes": 2015, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t0001", "version": null, "note": "Clinicopathologic Characteristics of HCC Patients in Training and Validation Cohorts", "structure": {"pmcid": "PMC8018394", "section_index": 12, "section_title": "Establishment of a Prognostic Metabolic-Related Gene Signature", "row_count": 37, "column_count": 5}, "table": {"label": "Table 1", "caption": "Clinicopathologic Characteristics of HCC Patients in Training and Validation Cohorts", "rows": [["Characteristics", "TCGA Cohort", "GSE14520 Cohort", "ICGC Cohort", "Clinical Cohort"], ["Samples sizea", "342", "242", "232", "64"], ["Median OS (year)", "1.61 (0.08–10.07)", "4.24 (0.15–5.54)", "2.14 (0.03–5.92)", "4.77 (0.47–5.10)"], ["Number of deaths", "119 (34.8%)", "96 (39.7%)", "43 (18.5%)", "35 (54.7%)"], ["Age (year)", "", "", "", ""], ["≤ 50", "73 (21.3%)", "125 (51.7%)", "17 (7.3%)", "19 (29.7%)"], ["> 50", "269 (78.7%)", "117 (48.3%)", "215 (92.7%)", "45 (70.3%)"], ["Gender", "", "", "", ""], ["Male", "233 (68.1%)", "211 (87.2%)", "171 (73.7%)", "60 (93.8%)"], ["Female", "109 (31.9%)", "31 (12.8%)", "61 (26.3%)", "4 (6.2%)"], ["TNM stage", "", "", "", ""], ["Stage I–II", "238 (74.1%)", "174 (77.3%)", "142 (61.2%)", "51 (79.7%)"], ["Stage III–IV", "83 (25.9%)", "51 (22.7%)", "90 (38.8%)", "13 (20.3%)"], ["AFP (ng/mL)", "", "", "", ""], ["≤ 300", "198 (76.2%)", "–", "–", "34 (53.1%)"], ["> 300", "62 (23.8%)", "–", "–", "30 (46.9%)"], ["Histologic grade", "", "", "", ""], ["G1-2", "214 (63.5%)", "–", "–", "39 (60.9%)"], ["G3-4", "123 (36.5%)", "–", "–", "25 (39.1%)"], ["Vascular invasion", "", "", "", ""], ["Absent", "187 (64.9%)", "–", "–", "57 (89.1%)"], ["Present", "101 (35.1%)", "–", "–", "7 (10.9%)"], ["Child-pugh score", "", "", "", ""], ["A", "204 (91.1%)", "–", "–", "62 (96.9%)"], ["B", "20 (8.9%)", "–", "–", "2 (3.1%)"], ["Tumor size (cm)", "", "", "", ""], ["≤ 5", "–", "153 (63.5%)", "–", "36 (56.3%)"], ["> 5", "–", "88 (36.5%)", "–", "28 (43.7%)"], ["Multinodular", "", "", "", ""], ["No", "–", "190 (78.5%)", "–", "49 (76.6%)"], ["Yes", "–", "52 (21.5%)", "–", "15 (23.4%)"], ["Cirrhosis", "", "", "", ""], ["Absent", "–", "19 (7.9%)", "–", "13 (20.3%)"], ["Present", "–", "223 (92.1%)", "–", "51 (79.7%)"], ["BCLC stage", "", "", "", ""], ["0-A", "–", "172 (76.4%)", "–", "36 (56.3%)"], ["B-C", "–", "53 (23.6%)", "–", "28 (43.7%)"]], "row_count": 37, "column_count": 5, "numeric_cells": 78, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:33824863:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:fb0fd900b3487912c5383dd8e85787f5473dbf5de6b162952b59b8c01858cc13", "bytes": 1090, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#t0002", "version": null, "note": "Description of 10 Metabolic-Related Genes Identified by LASSO Regression Analysis", "structure": {"pmcid": "PMC8018394", "section_index": 12, "section_title": "Establishment of a Prognostic Metabolic-Related Gene Signature", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Description of 10 Metabolic-Related Genes Identified by LASSO Regression Analysis", "rows": [["Gene", "Coefficient", "Description of the Encoded Protein"], ["HEXB", "0.006533217", "The beta subunit of beta-hexosaminidase"], ["CYP2C9", "−0.000601418", "A member of the cytochrome P450 superfamily"], ["ATIC", "0.02286243", "A protein involved in the de novo purine biosynthesis"], ["G6PD", "0.001574899", "Glucose-6-phosphate dehydrogenase"], ["LPCAT1", "0.008226413", "A member of the 1-acyl-sn-glycerol-3-phosphate acyltransferase family"], ["RRM1", "0.02908161", "The large and catalytic subunit of ribonucleotide reductase"], ["RRM2", "0.013628698", "One of two non-identical subunits for ribonucleotide reductase"], ["TXNRD1", "0.012162138", "A member of the pyridine nucleotide-disulfide oxidoreductase family"], ["ME1", "0.006466633", "An enzyme that generates NADPH for fatty acid biosynthesis"], ["ADH1C", "−0.001026019", "Class I alcohol dehydrogenase, gamma subunit"]], "row_count": 11, "column_count": 3, "numeric_cells": 13, "header_rows": 1, "locator": "section[12]/table-wrap[2]#t0002"}}, {"id": "asset:table:pmid:33824863:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:97d0a6002c6263963bd953ab8d21caf848166efd26f3c806207ab06a90c14a33", "bytes": 1085, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0003", "version": null, "note": "Correlation of Risk Score with Clinicopathologic Characteristics of HCC Patients in the TCGA Cohort", "structure": {"pmcid": "PMC8018394", "section_index": 13, "section_title": "The Risk-Stratification and Subtype-Identification Value of the Signature in HCC", "row_count": 23, "column_count": 4}, "table": {"label": "Table 3", "caption": "Correlation of Risk Score with Clinicopathologic Characteristics of HCC Patients in the TCGA Cohort", "rows": [["Characteristics", "TCGA Cohorta", "P valueb"], ["High Risk (n = 171)", "Low Risk (n = 171)"], ["Age (year)", "", "", "0.692"], ["≤ 50", "35 (20.5%)", "38 (22.2%)"], ["> 50", "136 (79.5%)", "133 (77.8%)"], ["Gender", "", "", "0.908"], ["Male", "117 (68.4%)", "116 (67.8%)"], ["Female", "54 (31.6%)", "55 (32.2%)"], ["TNM stage", "", "", "0.001"], ["Stage I–II", "107 (66.0%)", "131 (82.4%)"], ["Stage III–IV", "55 (34.0%)", "28 (17.6%)"], ["AFP (ng/mL)", "", "", "0.071"], ["≤ 300", "89 (71.2%)", "109 (80.7%)"], ["> 300", "36 (28.8%)", "26 (19.3%)"], ["Histologic grade", "", "", "< 0.001"], ["G1-2", "90 (53.3%)", "124 (73.8%)"], ["G3-4", "79 (46.7%)", "44 (26.2%)"], ["Vascular invasion", "", "", "0.001"], ["Absent", "76 (55.5%)", "111 (73.5%)"], ["Present", "61 (44.5%)", "40 (26.5%)"], ["Child-pugh score", "", "", "0.546"], ["A", "96 (92.3%)", "108 (90.0%)"], ["B", "8 (7.7%)", "12 (10.0%)"]], "row_count": 23, "column_count": 4, "numeric_cells": 43, "header_rows": 2, "locator": "section[13]/table-wrap[1]#t0003"}}], "gaps": ["asset:data:geo:GSE14520 not downloaded", "asset:data:geo:GSE14520 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The least absolute shrinkage and selection operator (LASSO) COX regression analysis was then conducted to construct the prognostic signature with 1000-fold cross-validation using the “glmnet” package in R software."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "logistic regression"}}, {"id": "method-3", "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"}}, {"id": "method-4", "family": "model_calibration", "specific": "decision_curve", "label": "Model calibration / clinical utility", "dsl_operations": ["calibration_bins", "net_benefit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictions_and_outcomes"], "evidence": {"score": 0.7, "band": "medium", "quote": "net benefit"}}, {"id": "method-5", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE14520"], "resolved_accessions": ["GSE14520"], "statements": ["Gene expression and clinical information of TCGA cohort were acquired from Genomic Data Commons Data Portal and cBioPortal for Cancer Genomics, respectively."], "basis": "The paper names GSE14520 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": ["cox_ph"], "assets": ["source:pmid:33824863", "data:geo:GSE14520", "asset:table:pmid:33824863:1", "asset:table:pmid:33824863:2", "asset:table:pmid:33824863:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14520"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 34264, "completion_tokens": 2104, "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:33824863", "type": "paper", "label": "pmid:33824863"}, {"id": "source:pmid:33824863", "type": "manuscript", "label": "PMID 33824863 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33824863", "type": "paper", "label": "pmid:33824863"}, {"id": "source:pmid:33824863", "type": "manuscript", "label": "PMID 33824863 full text"}, {"id": "data:geo:GSE14520", "type": "dataset", "label": "GEO GSE14520"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33824863", "type": "extraction", "used": ["source:pmid:33824863"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14520", "type": "accession_resolution", "used": ["data:geo:GSE14520"], "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:33824863", "parent_hash": "sha256:723236a8bc676ffabd813a415d432348a9999bc3f5507a702c7e6e279f5a1735", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE14520 licence not read", "asset:data:geo:GSE14520 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The least absolute shrinkage and selection operator (LASSO) COX regression analysis was then conducted to construct the prognostic signature with 1000-fold cross-validation using the “glmnet” package in R software."], "order_basis": "analysis_only", "id": "assay:1"}]}