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pmid:30148168

Downregulation of CYP2A6 and CYP2C8 in Tumor Tissues Is Linked to Worse Overall Survival and Recurrence-Free Survival from Hepatocellular Carcinoma.

Xiaojing Ren · Yuanyuan Ji · Xuhua Jiang · Xun Qi

BioMed research international · 2018 doi:10.1155/2018/5859415

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:30148168
kind
science-record
content_hash
sha256:1a7554f2ecea26541cbd6524a8c6b58e5f90452336d04877561841d489e854c8
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https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:36Z
updated_at
2026-11-01T22:43:30Z
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paper object · 10 fields
state
complete
title
Downregulation of CYP2A6 and CYP2C8 in Tumor Tissues Is Linked to Worse Overall Survival and Recurrence-Free Survival from Hepatocellular Carcinoma.
doi
10.1155/2018/5859415
pmid
30148168
authors array · 4 items
[0]
Xiaojing Ren
[1]
Yuanyuan Ji
[2]
Xuhua Jiang
[3]
Xun Qi
journal
BioMed research international
year
2018
abstract
OBJECTIVE: This study aimed to evaluate the links between CYP450 family genes in tumor tissues and hepatocellular carcinoma (HCC) outcomes. METHODS: Gene Expression Omnibus (GEO) databases GSE14520 and GSE36376 were used to identify differential expressed CYP450 genes between tumor and nontumor tissues and related to HCC clinicopathological features and survivals. RESULTS: Seven CYP450 genes including CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2E1, CYP3A4, and CYP4A11 were downregulated in tumor tissues, which were validated in both GSE14520 and GSE36376. HCC patients with CYP2A6 and CYP2C8 low levels in tumor tissues suffered from poorer overall survival (OS) compared to those with high CYP2A6 and CYP2C8 in GSE14520 profile (log ranks P = 0.01 and P = 0.006, respectively). In addition, HCC patients with lower CYP2A6 and CYP2C8 in tumors had worse recurrence-free survival (RFS) than those with higher CYP2A6 and CYP2C8 (log ranks P = 0.02 and P = 0.012, respectively). In GSE36376 validation dataset, HCC patients with lower CYP2A6 and CYP2C8 had worse OS and RFS than those with higher CYP2A6 and CYP2C8 (all P < 0.05), in line with results in GSE14520 dataset. Additionally, lower CYP2A6 and CYP2C8 are associated with advanced clinicopathological features including tumor staging, vascular invasion, intrahepatic metastasis, and high alpha fetoprotein (all P < 0.05). CONCLUSION: Downregulation of CYP2A6 and CYP2C8 in tumor tissues links to poorer OS and RFS in HCC patients.
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Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival.
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sections[7] "2.5. Statistical Analysis" paragraph 2
quote
Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival.
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All the data in this study were available from GEO database (https://www.ncbi.nlm.nih.gov/geo/).
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sections[14] "Data Availability" paragraph 2
quote
All the data in this study were available from GEO database (https://www.ncbi.nlm.nih.gov/geo/).
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https://doi.org/10.1155/2018/5859415
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Differential expressed CYP450 genes between tumor and nontumor tissues from GSE14520 and GSE36376.
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3.1. Differential Expressed CYPs in Both GSE14520 and GSE36376
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Table 1
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Differential expressed CYP450 genes between tumor and nontumor tissues from GSE14520 and GSE36376.
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[0] array · 7 items
[0]
Genes
[1]
t
[2]
B
[3]
log⁡FC
[4]
P value
[5]
Adjust P value
[6]
Common genes
[1] array · 7 items
[0]
GSE14520
[1]
[2]
[3]
[4]
[5]
[6]
CYP1A2CYP2A6CYP2C8CYP2C9CYP2E1CYP3A4 CYP4A11
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[0]
CYP1A2
[1]
25.7352762
[2]
49.901907
[3]
4.44705742
[4]
1.63E-22
[5]
7.31E-27
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[0]
CYP2A6
[1]
7.9627779
[2]
12.348032
[3]
3.07188278
[4]
3.66E-08
[5]
7.66E-10
[4] array · 6 items
[0]
CYP2B6
[1]
15.7936233
[2]
33.005014
[3]
3.89306938
[4]
6.65E-16
[5]
5.37E-19
[5] array · 6 items
[0]
CYP2B7P
[1]
24.284837
[2]
180.032064
[3]
3.5900407
[4]
1.8E-81
[5]
1.25E-83
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[0]
CYP2C8
[1]
6.4917335
[2]
7.665054
[3]
4.32698325
[4]
0.0000018
[5]
8.78E-08
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[0]
CYP2C9
[1]
23.3715192
[2]
46.568366
[3]
3.36577273
[4]
1.63E-21
[5]
2.93E-25
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8.2816633
[2]
13.340866
[3]
4.73015789
[4]
0.000000016
[5]
2.81E-10
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[0]
CYP3A4
[1]
7.9970664
[2]
12.45527
[3]
3.99461005
[4]
3.37E-08
[5]
6.87E-10
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[0]
CYP4A11
[1]
8.8192119
[2]
14.989899
[3]
3.11363397
[4]
3.99E-09
[5]
5.29E-11
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[0]
CYP4A22
[1]
8.6445676
[2]
14.457718
[3]
3.17968421
[4]
6.1E-09
[5]
9.06E-11
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[0]
CYP39A1
[1]
10.5703094
[2]
20.114355
[3]
3.19955263
[4]
5.84E-11
[5]
2.94E-13
[13] array · 6 items
[0]
GSE36376
[1]
[2]
[3]
[4]
[5]
[14] array · 6 items
[0]
CYP1A2
[1]
30.5006424
[2]
240.408848
[3]
4.97
[4]
1.29E-106
[5]
6.05E-110
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[0]
CYP2A6
[1]
15.0803249
[2]
83.643956
[3]
2.47
[4]
2.71E-40
[5]
1.3E-41
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[0]
CYP2C8
[1]
17.410711
[2]
107.141675
[3]
3.05
[4]
2.5E-50
[5]
7.36E-52
[17] array · 6 items
[0]
CYP2C9
[1]
14.9361339
[2]
82.220342
[3]
2.36
[4]
1.1E-39
[5]
5.44E-41
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[0]
CYP2E1
[1]
15.0716592
[2]
83.558278
[3]
3
[4]
2.95E-40
[5]
1.42E-41
[19] array · 6 items
[0]
CYP3A4
[1]
22.4720068
[2]
159.580681
[3]
3.91
[4]
1.3E-72
[5]
1.03E-74
[20] array · 6 items
[0]
CYP4A11
[1]
14.3069129
[2]
76.061125
[3]
2.06
[4]
4.62E-37
[5]
2.65E-38
[21] array · 6 items
[0]
CYP8B1
[1]
12.9803487
[2]
63.40673
[3]
2.18
[4]
1.18E-31
[5]
8.9E-33
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Clinicopathological comparison grouped by CYP2A6 and CYP2C8 from GSE14520 and GSE36376.
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3.4. Relationship between CYP2A6, CYP2C8, and HCC Clinicopathological Features
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Table 2
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Clinicopathological comparison grouped by CYP2A6 and CYP2C8 from GSE14520 and GSE36376.
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CYP2C8
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42/68
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0.583
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[4]
33/77/0
[5]
45/64/1
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0.091
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[2]
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0.181
[4]
21/89
[5]
24/86
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0.738
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[0]
Cirrhosis (yes/no)
[1]
101/9
[2]
101/9
[3]
1.0
[4]
101/9
[5]
101/9
[6]
1.0
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[0]
TNM staging (I/II/III/NA)
[1]
57/37/15/1
[2]
36/40/33/1
[3]
0.005
[4]
56/33/21/0
[5]
37/44/27/2
[6]
0.032
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[0]
BCLC staging (0-A/B/C/NA)
[1]
83/9/7/1
[2]
75/13/21/1
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0.039
[4]
79/8/13/0
[5]
79/14/15/2
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0.357
[10] array · 1 item
[0]
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GSE36376
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[2]
[3]
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Edmondson grade (I/II/III)
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8/97/15
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0.01
[4]
19/96/5
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5/101/14
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0.002
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[0]
Tumor size (median), mm
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34 (31)
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40 (45)
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0.203
[4]
34 (30)
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42 (45)
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0.081
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[0]
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84/36
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84/36
[6]
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[0]
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1/119
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8/112
[3]
0.036
[4]
1/119
[5]
8/112
[6]
0.036
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[0]
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38/82
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0.002
[4]
18/102
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37/83
[6]
0.005
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[0]
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8/112
[2]
5/115
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0.57
[4]
7/113
[5]
6/114
[6]
1.0
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[0]
Direct invasion of adjacent organ (yes/no)
[1]
3/117
[2]
2/118
[3]
1.0
[4]
3/117
[5]
2/118
[6]
1.0
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AJCC staging (1/2/3/4)
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36/57/25/2
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[4]
67/42/8/3
[5]
35/58/25/2
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75/43/2
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64/48/8
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0.092
[4]
80/38/2
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59/53/8
[6]
0.009
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[0]
Alpha fetoprotein [Median (IQR), ng/ml]
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9.65 (82.2)
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256.6 (4136.8)
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<0.001
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303.8 (9534.45)
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<0.001
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Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival.
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data:geo:None
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agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
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 object · 4 fields
parent_id
pmid:30148168
parent_hash
sha256:dd4ece88c47406d8746d831fecf8e4d5237ab7870c8e2db83b84a299fa8cd314
fork_of
null
gaps array · 7 items
[0]
execution.not_run
[1]
method.student_t
[2]
review.human_critique
[3]
review.independent_reader
[4]
review.machine_critique
[5]
step:obtain_source_data blocked on data:accession_absent
[6]
step:run_analysis blocked on method:student_t
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival.
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30148168", "kind": "science-record", "revision": 8, "content_hash": "sha256:1a7554f2ecea26541cbd6524a8c6b58e5f90452336d04877561841d489e854c8", "created_at": "2026-11-01T15:40:36Z", "updated_at": "2026-11-01T22:43:30Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Downregulation of CYP2A6 and CYP2C8 in Tumor Tissues Is Linked to Worse Overall Survival and Recurrence-Free Survival from Hepatocellular Carcinoma.", "doi": "10.1155/2018/5859415", "pmid": "30148168", "authors": ["Xiaojing Ren", "Yuanyuan Ji", "Xuhua Jiang", "Xun Qi"], "journal": "BioMed research international", "year": 2018, "abstract": "OBJECTIVE: This study aimed to evaluate the links between CYP450 family genes in tumor tissues and hepatocellular carcinoma (HCC) outcomes.\nMETHODS: Gene Expression Omnibus (GEO) databases GSE14520 and GSE36376 were used to identify differential expressed CYP450 genes between tumor and nontumor tissues and related to HCC clinicopathological features and survivals.\nRESULTS: Seven CYP450 genes including CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2E1, CYP3A4, and CYP4A11 were downregulated in tumor tissues, which were validated in both GSE14520 and GSE36376. HCC patients with CYP2A6 and CYP2C8 low levels in tumor tissues suffered from poorer overall survival (OS) compared to those with high CYP2A6 and CYP2C8 in GSE14520 profile (log ranks P = 0.01 and P = 0.006, respectively). In addition, HCC patients with lower CYP2A6 and CYP2C8 in tumors had worse recurrence-free survival (RFS) than those with higher CYP2A6 and CYP2C8 (log ranks P = 0.02 and P = 0.012, respectively). In GSE36376 validation dataset, HCC patients with lower CYP2A6 and CYP2C8 had worse OS and RFS than those with higher CYP2A6 and CYP2C8 (all P < 0.05), in line with results in GSE14520 dataset. Additionally, lower CYP2A6 and CYP2C8 are associated with advanced clinicopathological features including tumor staging, vascular invasion, intrahepatic metastasis, and high alpha fetoprotein (all P < 0.05).\nCONCLUSION: Downregulation of CYP2A6 and CYP2C8 in tumor tissues links to poorer OS and RFS in HCC patients.", "claims": [{"id": "claim-method", "statement": "Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30148168", "locator": "sections[7] \"2.5. Statistical Analysis\" paragraph 2", "quote": "Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data in this study were available from GEO database (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30148168", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "All the data in this study were available from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."}], "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:30148168"], "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": "blocked", "blocked_on": "method:student_t", "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:run_analysis blocked on method:student_t", "step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30148168", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2018/5859415", "sha256": "sha256:b933a5b4dbc708672d9e05bf5d41a5d4bd89b2d0755ed99245aead5eee99282e", "bytes": 24297, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2018/5859415", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6083600", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30148168:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ec8ddb1be41594645c1e8f462bf808d9c87b390dafcd6b359ca3722c8199c152", "bytes": 1717, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tab1", "version": null, "note": "Differential expressed CYP450 genes between tumor and nontumor tissues from GSE14520 and GSE36376.", "structure": {"pmcid": "PMC6083600", "section_index": 9, "section_title": "3.1. Differential Expressed CYPs in Both GSE14520 and GSE36376", "row_count": 22, "column_count": 7}, "table": {"label": "Table 1", "caption": "Differential expressed CYP450 genes between tumor and nontumor tissues from GSE14520 and GSE36376.", "rows": [["Genes", "t", "B", "log⁡FC", "P value", "Adjust P value", "Common genes"], ["GSE14520", "", "", "", "", "", "CYP1A2CYP2A6CYP2C8CYP2C9CYP2E1CYP3A4 CYP4A11"], ["CYP1A2", "25.7352762", "49.901907", "4.44705742", "1.63E-22", "7.31E-27"], ["CYP2A6", "7.9627779", "12.348032", "3.07188278", "3.66E-08", "7.66E-10"], ["CYP2B6", "15.7936233", "33.005014", "3.89306938", "6.65E-16", "5.37E-19"], ["CYP2B7P", "24.284837", "180.032064", "3.5900407", "1.8E-81", "1.25E-83"], ["CYP2C8", "6.4917335", "7.665054", "4.32698325", "0.0000018", "8.78E-08"], ["CYP2C9", "23.3715192", "46.568366", "3.36577273", "1.63E-21", "2.93E-25"], ["CYP2E1", "8.2816633", "13.340866", "4.73015789", "0.000000016", "2.81E-10"], ["CYP3A4", "7.9970664", "12.45527", "3.99461005", "3.37E-08", "6.87E-10"], ["CYP4A11", "8.8192119", "14.989899", "3.11363397", "3.99E-09", "5.29E-11"], ["CYP4A22", "8.6445676", "14.457718", "3.17968421", "6.1E-09", "9.06E-11"], ["CYP39A1", "10.5703094", "20.114355", "3.19955263", "5.84E-11", "2.94E-13"], ["GSE36376", "", "", "", "", ""], ["CYP1A2", "30.5006424", "240.408848", "4.97", "1.29E-106", "6.05E-110"], ["CYP2A6", "15.0803249", "83.643956", "2.47", "2.71E-40", "1.3E-41"], ["CYP2C8", "17.410711", "107.141675", "3.05", "2.5E-50", "7.36E-52"], ["CYP2C9", "14.9361339", "82.220342", "2.36", "1.1E-39", "5.44E-41"], ["CYP2E1", "15.0716592", "83.558278", "3", "2.95E-40", "1.42E-41"], ["CYP3A4", "22.4720068", "159.580681", "3.91", "1.3E-72", "1.03E-74"], ["CYP4A11", "14.3069129", "76.061125", "2.06", "4.62E-37", "2.65E-38"], ["CYP8B1", "12.9803487", "63.40673", "2.18", "1.18E-31", "8.9E-33"]], "row_count": 22, "column_count": 7, "numeric_cells": 102, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:30148168:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7e9af7c9cda61ef745ebf42abeee41cd37b000c6a2e543b01ec8d999577e8767", "bytes": 1894, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab2", "version": null, "note": "Clinicopathological comparison grouped by CYP2A6 and CYP2C8 from GSE14520 and GSE36376.", "structure": {"pmcid": "PMC6083600", "section_index": 12, "section_title": "3.4. Relationship between CYP2A6, CYP2C8, and HCC Clinicopathological Features", "row_count": 22, "column_count": 7}, "table": {"label": "Table 2", "caption": "Clinicopathological comparison grouped by CYP2A6 and CYP2C8 from GSE14520 and GSE36376.", "rows": [["Category", "CYP2A6", "P value", "CYP2C8", "P value"], ["High", "Low", "High", "Low"], ["GSE14520", "", "", "", "", "", ""], ["HBV viral status (AVR-CC/CC/NA)", "25/81/4", "31/74/5", "0.635", "28/78/4", "28/77/5", "0.943"], ["Alanine aminotransferase (>50/<50, U/L)", "38/72", "51/59", "0.099", "42/68", "47/63", "0.583"], ["Main tumor size (>5/<5/NA, cm)", "34/76/0", "44/65/1", "0.16", "33/77/0", "45/64/1", "0.091"], ["Multinodular (yes/no)", "18/92", "27/83", "0.181", "21/89", "24/86", "0.738"], ["Cirrhosis (yes/no)", "101/9", "101/9", "1.0", "101/9", "101/9", "1.0"], ["TNM staging (I/II/III/NA)", "57/37/15/1", "36/40/33/1", "0.005", "56/33/21/0", "37/44/27/2", "0.032"], ["BCLC staging (0-A/B/C/NA)", "83/9/7/1", "75/13/21/1", "0.039", "79/8/13/0", "79/14/15/2", "0.357"], [""], ["GSE36376", "", "", "", "", "", ""], ["Edmondson grade (I/II/III)", "16/100/4", "8/97/15", "0.01", "19/96/5", "5/101/14", "0.002"], ["Tumor size (median), mm", "34 (31)", "40 (45)", "0.203", "34 (30)", "42 (45)", "0.081"], ["Vascular invasion (yes/no)", "51/69", "84/36", "<0.001", "51/69", "84/36", "<0.001"], ["Major portal vein invasion (yes/no)", "1/119", "8/112", "0.036", "1/119", "8/112", "0.036"], ["Intrahepatic metastasis (yes/no)", "17/103", "38/82", "0.002", "18/102", "37/83", "0.005"], ["Multicentric occurrence (yes/no)", "8/112", "5/115", "0.57", "7/113", "6/114", "1.0"], ["Direct invasion of adjacent organ (yes/no)", "3/117", "2/118", "1.0", "3/117", "2/118", "1.0"], ["AJCC staging (1/2/3/4)", "66/43/8/3", "36/57/25/2", "<0.001", "67/42/8/3", "35/58/25/2", "<0.001"], ["BCLC staging (A/B/C)", "75/43/2", "64/48/8", "0.092", "80/38/2", "59/53/8", "0.009"], ["Alpha fetoprotein [Median (IQR), ng/ml]", "9.65 (82.2)", "256.6 (4136.8)", "<0.001", "9.1 (61.6)", "303.8 (9534.45)", "<0.001"]], "row_count": 22, "column_count": 7, "numeric_cells": 108, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tab2"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. The Kaplan–Meier method was used to compare survivals between different groups, and the log-rank test was used to estimate the difference in survival."}}, {"id": "method-2", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_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": ["All the data in this study were available from GEO database (https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30148168", "asset:table:pmid:30148168:1", "asset:table:pmid:30148168:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "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": "2026-10-31T18:35:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 21909, "completion_tokens": 1364, "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:30148168", "type": "paper", "label": "pmid:30148168"}, {"id": "source:pmid:30148168", "type": "manuscript", "label": "PMID 30148168 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30148168", "type": "paper", "label": "pmid:30148168"}, {"id": "source:pmid:30148168", "type": "manuscript", "label": "PMID 30148168 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30148168", "type": "extraction", "used": ["source:pmid:30148168"], "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:30148168", "parent_hash": "sha256:dd4ece88c47406d8746d831fecf8e4d5237ab7870c8e2db83b84a299fa8cd314", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Student's t-test was used to compare means for normally distributed continuous data, and the Mann–Whitney U test was used for nonnormally distributed continuous data and the Chi-squared test was used for categorical variables. 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