← All .science files
pmid:30814912
Expression of the Wnt ligands gene family and its relationship to prognosis in hepatocellular carcinoma.
Jia-Jia Dong · Li Ying · Ke-Qing Shi
Cancer cell international · 2019 doi:10.1186/s12935-019-0743-z
Paper
complete
Experiment
partial
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 · 3 items
claims array · 2 items
[0] object · 6 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 · 0 items
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 0 items
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 · 1 item
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 3 items
[1] array · 10 items
[2] array · 1 item
[3] array · 11 items
[4] array · 11 items
[5] array · 1 item
[6] array · 11 items
[7] array · 11 items
[8] array · 1 item
[9] array · 11 items
[10] array · 11 items
[11] array · 11 items
[12] array · 1 item
[13] array · 11 items
[14] array · 11 items
[15] array · 11 items
[16] array · 1 item
[17] array · 11 items
[18] array · 11 items
[19] array · 11 items
[20] array · 1 item
[21] array · 11 items
[22] array · 11 items
[23] array · 11 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 52 items
[0] array · 5 items
[1] array · 4 items
[2] array · 7 items
[3] array · 6 items
[4] array · 7 items
[5] array · 6 items
[6] array · 7 items
[7] array · 6 items
[8] array · 7 items
[9] array · 6 items
[10] array · 7 items
[11] array · 6 items
[12] array · 7 items
[13] array · 6 items
[14] array · 7 items
[15] array · 6 items
[16] array · 7 items
[17] array · 6 items
[18] array · 7 items
[19] array · 6 items
[20] array · 7 items
[21] array · 6 items
[22] array · 7 items
[23] array · 6 items
[24] array · 7 items
[25] array · 6 items
[26] array · 7 items
[27] array · 6 items
[28] array · 7 items
[29] array · 6 items
[30] array · 7 items
[31] array · 6 items
[32] array · 7 items
[33] array · 6 items
[34] array · 7 items
[35] array · 6 items
[36] array · 7 items
[37] array · 6 items
[38] array · 7 items
[39] array · 6 items
[40] array · 7 items
[41] array · 6 items
[42] array · 7 items
[43] array · 6 items
[44] array · 7 items
[45] array · 6 items
[46] array · 7 items
[47] array · 6 items
[48] array · 7 items
[49] array · 6 items
[50] array · 7 items
[51] array · 6 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 12 items
[1] array · 10 items
[2] array · 1 item
[3] array · 17 items
[4] array · 17 items
[5] array · 1 item
[6] array · 17 items
[7] array · 17 items
[8] array · 1 item
[9] array · 17 items
[10] array · 17 items
[11] array · 17 items
[12] array · 1 item
[13] array · 17 items
[14] array · 17 items
[15] array · 17 items
[16] array · 1 item
[17] array · 17 items
[18] array · 17 items
[19] array · 17 items
[20] array · 1 item
[21] array · 17 items
[22] array · 17 items
[23] array · 17 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 4 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
gaps array · 0 items
analysis object · 4 fields
methods array · 4 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 · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] 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 · 0 items
resolved_accessions array · 0 items
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 · 1 item
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 · 5 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 2 items
[1] 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:30814912", "kind": "science-record", "revision": 6, "content_hash": "sha256:f12c82d40095c95742b55a0afc17175019c6fec6e509180780ece76457d83551", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T21:22:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression of the Wnt ligands gene family and its relationship to prognosis in hepatocellular carcinoma.", "doi": "10.1186/s12935-019-0743-z", "pmid": "30814912", "authors": ["Jia-Jia Dong", "Li Ying", "Ke-Qing Shi"], "journal": "Cancer cell international", "year": 2019, "abstract": "BACKGROUND: The Wnt gene family members are known to participate regulating various normal and pathological processes including tumorigenesis. However, the association between Wnt ligands gene family and prognosis in hepatocellular carcinoma has not been systematically studied. Therefore, we evaluated the role of Wnt ligands gene family in hepatocellular carcinoma using publicly available data from The Cancer Genome Atlas (TCGA).\nMETHODS: Clinical information and RNA-Seq mRNA expression data were derived from TCGA hepatocellular carcinoma cohort. Differences in overall survival (OS) and disease-free survival (DFS) between increased and decreased expression groups (defined by X-tile analyses) of Wnt ligands gene family were compared using Kaplan-Meier method and Cox regression model, with p-values calculated via log-rank test. Gene Set Enrichment Analysis (GSEA) was performed.\nRESULTS: Multivariate analysis adjusted for patient age, sex, BMI, tumor grade, and TMN stage revealed that Wnt1, Wnt3 and Wnt5B expressions were independent prognostic factors for OS and DFS (OS: HR = 0.58, P = 0.006; HR = 0.65, P = 0.03; HR = 0.56, P = 0.023, respectively; DFS: HR = 0.52, P < 0.001; HR = 1.93, P = 0.003; HR = 0.59, P = 0.011, respectively). Furthermore, expression of Wnt1 and Wnt5B was significantly associated with TMN stage (P = 0.02 and P = 0.03 for OS; P = 0.02 and P = 0.02 for DFS). GSEA showed that nucleotide excision repair was differentially enriched in Wnt1 low expression phenotype and aminoacyl trna biosynthesis and basal transcription factors were differentially enriched in Wnt5B low expression phenotype.\nCONCLUSIONS: Our results identified associations of several Wnt ligands with prognosis of HCC patients, indicating that these genes could serve as prognostic biomarkers of HCC.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier survival analysis and log-rank test were used to compare differences in survival times.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30814912", "locator": "sections[4] \"Statistical analysis\" paragraph 2", "quote": "The Kaplan–Meier survival analysis and log-rank test were used to compare differences in survival times."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analysed during the current study are available in the TCGA Research Network: http://cancergenome.nih.gov/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30814912", "locator": "sections[15] \"ack\" paragraph 1", "quote": "The datasets generated and/or analysed during the current study are available in the TCGA Research Network: http://cancergenome.nih.gov/."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30814912"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30814912", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-019-0743-z", "sha256": "sha256:b6d9d1b7b0ece11ecdc0bec65690d25072c0bb7655f12770afecabdfd2eb7fa7", "bytes": 29206, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-019-0743-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6376661", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30814912:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:81b6049cb29e7b137871574f3c4981c6f28f6dd6688949755a85deebbe8647c5", "bytes": 1855, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#Tab1", "version": null, "note": "Basic characteristics of TCGA HCC patients", "structure": {"pmcid": "PMC6376661", "section_index": 6, "section_title": "Basic patient characteristics", "row_count": 24, "column_count": 11}, "table": {"label": "Table 1", "caption": "Basic characteristics of TCGA HCC patients", "rows": [["Clinical features", "Overall survival", "Disease-free survival"], ["Patients(n = 360)", "No.of events (%)", "MST (months)", "HR (95% CI)", "P value", "Patients(n = 310)", "No. of events (%)", "MST (month)", "HR (95% CI)", "P value"], ["Age (year)"], ["< 60", "165", "54 (32.7%)", "26.96", "1.18 (0.83–1.68)", "0.36", "145", "78 (53.8%)", "20.54", "0.78 (0.74–1.36)", "0.98"], ["≥ 60", "195", "75 (38.4%)", "26.39", "", "", "165", "92 (55.7%)", "19.75", "", ""], ["Sex"], ["Male", "243", "79 (32.5%)", "25.94", "1.18 (0.82–1.69)", "0.38", "203", "114 (56.1%)", "20.29", "0.84 (0.64–1.22)", "0.45"], ["Female", "117", "50 (42.7%)", "28.12", "", "", "97", "56 (57.7%)", "19.74", "", ""], ["Race"], ["Asian", "155", "44 (28.3%)", "25.87", "0.75 (0.52–1.09)", "0.13", "138", "69 (50.0%)", "21.26", "0.80 (0.59–1.09)", "0.16"], ["White + others", "195", "80 (41.0%)", "27.51", "", "", "165", "98 (59.4%)", "19.37", "", ""], ["Missing", "10", "", "", "", "", "7", "", "", "", ""], ["BMI"], ["≤ 25", "174", "62 (35.6%)", "25.30", "0.74 (0.51–1.06)", "0.10", "149", "80 (53.7%)", "18.50", "0.85 (0.62–1.18)", "0.33"], ["> 25", "153", "49 (32.0%)", "29.63", "", "", "135", "75 (55.5%)", "23.09", "", ""], ["Missing", "33", "", "", "", "", "26", "", "", "", ""], ["Grade"], ["1–2", "224", "78 (34.8%)", "27.13", "1.14 (0.78–1.67)", "0.49", "192", "101 (52.6%)", "20.22", "1.17 (0.85–1.61)", "0.33"], ["3–4", "131", "47 (35.8%)", "25.57", "", "", "114", "65 (57.1%)", "19.99", "", ""], ["Missing", "5", "", "", "", "", "4", "", "", "", ""], ["TNM stage"], ["I–II", "248", "67 (27.0%)", "28.34", "2.48 (1.71–3.62)", "<0.001", "215", "101 (46.9%)", "22.41", "2.41 (1.72–3.36)", "<0.001"], ["III–IV", "88", "48 (54.5%)", "22.54", "", "", "74", "55 (74.3%)", "14.58", "", ""], ["Missing", "24", "", "", "", "", "21", "", "", "", ""]], "row_count": 24, "column_count": 11, "numeric_cells": 114, "header_rows": 2, "locator": "section[6]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30814912:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9e20569e5657dda06c13ec623bac098dab067cf58e545feb64349423e4e75824", "bytes": 3221, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab2", "version": null, "note": "Univariate and multivariate analysis of overall survival using the Cox proportional hazard regression model", "structure": {"pmcid": "PMC6376661", "section_index": 8, "section_title": "Multivariate analysis and survival outcomes", "row_count": 52, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate and multivariate analysis of overall survival using the Cox proportional hazard regression model", "rows": [["Variables", "Category", "N", "Univariate analysis", "Multivariate analysis"], ["HR (95% CI)", "p Value", "HR (95% CI)", "p-Value"], ["Age", "< 60", "165", "1.18 (0.83–1.68)", "0.36", "", ""], ["≥ 60", "195", "", "", "", ""], ["Sex", "Male", "243", "1.18 (0.82–1.69)", "0.38", "", ""], ["Female", "117", "", "", "", ""], ["Race", "Asian", "155", "0.75 (0.52–1.09)", "0.13", "", ""], ["White + others", "195", "", "", "", ""], ["BMI", "≤25", "174", "0.74 (0.51–1.06)", "0.10", "", ""], [">25", "153", "", "", "", ""], ["Grade", "1–2", "224", "1.14 (0.78–1.67)", "0.49", "", ""], ["3–4", "131", "", "", "", ""], ["TNM stage", "I–II", "248", "2.48 (1.71–3.62)", "< 0.001", "2.02 (1.37–2.96)", "< 0.001"], ["III–IV", "88", "", "", "", ""], ["Wnt1", "Decreased (0–0.87)", "175", "0.50 (0.35–0.72)", "< 0.001", "0.58 (0.39–0.85)", "0.006"], ["Increased (> 0.87)", "185", "", "", "", ""], ["Wnt2", "Decreased (0–1.62)", "196", "1.42 (1.00–2.00)", "0.05", "", ""], ["Increased (> 1.66)", "164", "", "", "", ""], ["Wnt2B", "Decreased (0–4.12)", "188", "1.29 (0.91–1.82)", "0.19", "", ""], ["Increased (> 4.12)", "172", "", "", "", ""], ["Wnt3", "Decreased (2.58–37.97)", "140", "0.64 (0.45–0.91)", "0.01", "0.65 (0.45–0.96)", "0.03"], ["Increased (> 37.97)", "220", "", "", "", ""], ["Wnt3A", "Decreased (0–3.51)", "258", "1.32 (0.91–1.90)", "0.15", "", ""], ["Increased (> 3.51)", "102", "", "", "", ""], ["Wnt4", "Decreased (0–8.11)", "99", "1.49 (0.97–2.30)", "0.07", "", ""], ["Increased (> 8.11)", "261", "", "", "", ""], ["Wnt5A", "Decreased (0–416.79)", "301", "1.38 (0.87–2.16)", "0.17", "", ""], ["Increased (> 416.79)", "59", "", "", "", ""], ["Wnt5B", "Decreased (0.99–15.15)", "58", "0.51 (0.32–0.79)", "0.003", "0.56 (0.34–0.93)", "0.023"], ["Increased (> 15.15)", "302", "", "", "", ""], ["Wnt6", "Decreased (0–9.01)", "302", "1.61 (1.08–2.41)", "0.02", "1.62 (1.05–2.51)", "0.03"], ["Increased (> 9.01)", "58", "", "", "", ""], ["Wnt7A", "Decreased (0–0.24)", "216", "1.28 (0.90–1.82)", "0.17", "", ""], ["Increased (> 0.24)", "144", "", "", "", ""], ["Wnt7B", "Decreased (0–4.01)", "239", "1.42 (0.99–2.02)", "0.05", "", ""], ["Increased (> 4.01)", "121", "", "", "", ""], ["Wnt8A", "Decreased (0)", "351", "4.14 (1.51–11.3)", "0.006", "4.14 (1.47–11.68)", "0.007"], ["Increased (> 0)", "9", "", "", "", ""], ["Wnt8B", "Decreased (0–2.17)", "313", "1.35 (0.84–2.15)", "0.21", "", ""], ["Increased (> 2.17)", "47", "", "", "", ""], ["Wnt9A", "Decreased (0–0.24)", "183", "1.34 (0.95–1.90)", "0.10", "", ""], ["Increased (> 0.24)", "177", "", "", "", ""], ["Wnt9B", "Decreased (0–2.19)", "259", "0.78 (0.52–1.16)", "0.22", "", ""], ["Increased (> 2.19)", "101", "", "", "", ""], ["Wnt10A", "Decreased (0–4.38)", "186", "0.99 (0.99–1.01)", "0.80", "", ""], ["Increased (4.38–173.47)", "174", "", "", "", ""], ["Wnt10B", "Decreased (0–6.16)", "246", "0.70 (0.47–1.03)", "0.07", "", ""], ["Increased (> 6.16)", "114", "", "", "", ""], ["Wnt11", "Decreased (0–28.88)", "155", "0.70 (0.49–0.99)", "0.05", "", ""], ["Increased (> 28.88)", "205", "", "", "", ""], ["Wnt16", "Decreased (0–1.62)", "274", "1.43 (0.97–2.13)", "0.07", "", ""], ["Increased (> 1.66)", "86", "", "", "", ""]], "row_count": 52, "column_count": 7, "numeric_cells": 162, "header_rows": 2, "locator": "section[8]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:30814912:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4516dc10904df1dd9df6708e2edba0b5975e32d59e1a932d780eb929b903bb1a", "bytes": 1972, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab3", "version": null, "note": "Correlation of clinicopathologic variables and expression of several specific Wnts significantly associated with OS", "structure": {"pmcid": "PMC6376661", "section_index": 9, "section_title": "Association with Wnt ligands expression and clinicopathologic variables", "row_count": 24, "column_count": 17}, "table": {"label": "Table 3", "caption": "Correlation of clinicopathologic variables and expression of several specific Wnts significantly associated with OS", "rows": [["Clinical features", "Patients(n = 360)", "Wnt 1", "P value", "Wnt 3", "P value", "Wnt 5B", "P value", "Wnt 6", "P value", "Wnt 8A", "P value"], ["Decreased", "Increased", "Decreased", "Increased", "Decreased", "Increased", "Decreased", "Increased", "Decreased", "Increased"], ["Age (year)"], ["< 60", "165", "81", "84", "0.87", "67", "98", "0.54", "24", "141", "0.46", "136", "29", "0.49", "159", "6", "0.20"], ["≥ 60", "195", "94", "101", "", "73", "122", "", "34", "161", "", "166", "29", "", "192", "3", ""], ["Sex"], ["Male", "243", "124", "119", "0.19", "98", "145", "0.42", "41", "202", "0.57", "204", "39", "0.96", "237", "6", "0.95"], ["Female", "117", "51", "66", "", "42", "75", "", "17", "100", "", "98", "19", "", "114", "3", ""], ["Race"], ["Asian", "155", "77", "78", "0.64", "64", "91", "0.46", "29", "126", "0.22", "130", "25", "0.94", "153", "2", "0.17"], ["White + others", "195", "92", "103", "", "73", "122", "", "27", "168", "", "163", "32", "", "188", "7", ""], ["Missing", "10", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["BMI"], ["≤ 25", "174", "84", "90", "0.98", "68", "106", "0.64", "33", "141", "0.15", "143", "31", "0.40", "172", "2", "0.32"], ["> 25", "153", "74", "79", "", "56", "97", "", "20", "133", "", "131", "22", "", "149", "4", ""], ["Missing", "33", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["Grade"], ["1–2", "224", "107", "117", "0.53", "78", "146", "0.04", "37", "187", "0.75", "183", "41", "0.19", "221", "3", "0.06"], ["3–4", "131", "67", "64", "", "60", "71", "", "20", "111", "", "114", "17", "", "125", "6", ""], ["Missing", "5", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["TNM stage"], ["I–II", "248", "110", "138", "0.02", "99", "149", "0.69", "33", "215", "0.03", "207", "41", "0.89", "243", "5", "0.21"], ["III–IV", "88", "52", "36", "", "33", "55", "", "20", "68", "", "74", "14", "", "84", "4", ""], ["Missing", "24", "", "", "", "", "", "", "", "", "", "", "", "", "", "", ""]], "row_count": 24, "column_count": 17, "numeric_cells": 178, "header_rows": 2, "locator": "section[9]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:30814912:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3cb9e05bb8d065ce078912d018aa1b6fcd912f622bcbe817e568fdef8f14db48", "bytes": 521, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab4", "version": null, "note": "Gene sets enriched in decreased expression phenotype", "structure": {"pmcid": "PMC6376661", "section_index": 10, "section_title": "GSEA identifies a Wnt1-related and Wnt5B-related KEGG signaling pathway", "row_count": 4, "column_count": 6}, "table": {"label": "Table 4", "caption": "Gene sets enriched in decreased expression phenotype", "rows": [["MSigDB collection", "Gene", "Gene set name", "NES", "NOM p-val", "FDR q-val"], ["c2.cp.kegg.v6.1.entrez.gmt", "Wnt1", "KEGG_NUCLEOTIDE_EXCISION_REPAIR", "− 1.88", "0.002", "0.225"], ["", "Wnt5B", "KEGG_AMINOACYL_TRNA_BIOSYNTHESIS", "− 2.23", "0.000", "0.000"], ["", "", "KEGG_BASAL_TRANSCRIPTION_FACTORS", "− 1.74", "0.009", "0.248"]], "row_count": 4, "column_count": 6, "numeric_cells": 10, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab4"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Kaplan–Meier survival analysis and log-rank test were used to compare differences in survival times."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The datasets generated and/or analysed during the current study are available in the TCGA Research Network: http://cancergenome.nih.gov/."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:30814912", "asset:table:pmid:30814912:1", "asset:table:pmid:30814912:2", "asset:table:pmid:30814912:3", "asset:table:pmid:30814912:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "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": 24311, "completion_tokens": 1246, "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:30814912", "type": "paper", "label": "pmid:30814912"}, {"id": "source:pmid:30814912", "type": "manuscript", "label": "PMID 30814912 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30814912", "type": "paper", "label": "pmid:30814912"}, {"id": "source:pmid:30814912", "type": "manuscript", "label": "PMID 30814912 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30814912", "type": "extraction", "used": ["source:pmid:30814912"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:30814912", "parent_hash": "sha256:c28d0a3c1d48d476a89c6e3fa41f33618dda17466bbc5dc9e322e16af8e504a2", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["as (TCGA). METHODS: Clinical information and RNA-Seq mRNA expression data were derived from TCGA", "f biospecimen collection, RNA isolation, and RNA sequencing were previously described by the Cancer Geno"], "order_basis": "paper_text_order:528", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Kaplan–Meier survival analysis and log-rank test were used to compare differences in survival times."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}