Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:27672238

TBL1XR1 Is Highly Expressed in Gastric Cancer and Predicts Poor Prognosis.

Fang Liu · Yuan He · Qinghua Cao · Ni Liu · Wenhui Zhang

Disease markers · 2016 doi:10.1155/2016/2436518

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

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
id
pmid:27672238
kind
science-record
content_hash
sha256:b89eecb980cbdc8612ef1a4ec4d9f387c694bf7c8ba8b75509caba8786aa13ef
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:20Z
updated_at
2026-11-01T21:20:40Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
TBL1XR1 Is Highly Expressed in Gastric Cancer and Predicts Poor Prognosis.
doi
10.1155/2016/2436518
pmid
27672238
authors array · 5 items
[0]
Fang Liu
[1]
Yuan He
[2]
Qinghua Cao
[3]
Ni Liu
[4]
Wenhui Zhang
journal
Disease markers
year
2016
abstract
Objective. To investigate the expression of transducin- (β-) like 1 X-linked receptor 1 (TBL1XR1) in human gastric cancer (GC) and its correlation with prognostic and biologic significance. Methods. TBL1XR1 mRNA expression was analyzed in gastric cancer using a microarray dataset (GSE2701) from the Gene Expression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on GC tissue microarray (TMA) to assess its prognostic and biological significance in 334 patients of GC. Results. Analysis of GSE2701 showed that the mRNA levels of TBL1XR1 were significantly elevated in primary gastric tumor and lymph node tissues than normal gastric tissues (P < 0.05). The same results of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues. 204 of 334 (60.1%) primary gastric cancer tissues showed high expression of TBL1XR1 protein. TBL1XR1 overexpression was significantly correlated with lymph node metastasis (P = 0.000) and advanced TNM stage (P = 0.001). Moreover, high levels of TBL1XR1 predicted worse overall survival (P = 0.015). Multivariate Cox regression analysis indicated that high expression of TBL1XR1 was an independent prognostic factor for poor overall survival (HR, 0.525; 95% confidence interval, 0.367-0.752; P = 0.005). Conclusion. This present study demonstrates that TBL1XR1 is overexpressed in gastric cancer and may be a potential predictor and therapeutic target for GC patients.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:27672238
locator
sections[7] "2.5. Statistical Analysis" paragraph 2
quote
The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:27672238
locator
sections[3] "2.1. Gene Expression Profile Data of GSE2701" paragraph 2
quote
Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).
state
complete
[2] object · 6 fields
id
claim-target-result
statement
TBL1XR1 was overexpressed in gastric cancer, and its overexpression was associated with lymph node metastasis, advanced TNM stage, and poor overall survival.
kind
qualitative
target
null
evidence array · 4 items
[0] object · 3 fields
asset
source:pmid:27672238
locator
sections[0] "Abstract" paragraph 1
quote
Analysis of GSE2701 showed that the mRNA levels of TBL1XR1 were significantly elevated in primary gastric tumor and lymph node tissues than normal gastric tissues (P < 0.05).
[1] object · 3 fields
asset
source:pmid:27672238
locator
sections[0] "Abstract" paragraph 1
quote
The same results of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues.
[2] object · 3 fields
asset
source:pmid:27672238
locator
sections[0] "Abstract" paragraph 1
quote
TBL1XR1 overexpression was significantly correlated with lymph node metastasis (P = 0.000) and advanced TNM stage (P = 0.001).
[3] object · 3 fields
asset
source:pmid:27672238
locator
sections[0] "Abstract" paragraph 1
quote
Moreover, high levels of TBL1XR1 predicted worse overall survival (P = 0.015).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
TBL1XR1 was overexpressed in gastric cancer, and its overexpression was associated with lymph node metastasis, advanced TNM stage, and poor overall survival.
steps array · 3 items
[0] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:27672238
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE2701
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE2701
outputs array · 1 item
[0]
the replicated result and its comparison
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
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:27672238
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1155/2016/2436518
sha256
sha256:7149c699cd03b135e1948ad9f1cc1de05c46bd83e90a9f7e2f36a144e2039761
bytes
17953
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1155/2016/2436518
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC5031846
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE2701
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=GSE2701
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE2701
version
null
note
Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).
access_statement_kind
repository_route_statement
sample_accessions array · 126 items
[0]
GSM52188
[1]
GSM52189
[2]
GSM52190
[3]
GSM52191
[4]
GSM52192
[5]
GSM52193
[6]
GSM52194
[7]
GSM52195
[8]
GSM52196
[9]
GSM52197
[10]
GSM52198
[11]
GSM52199
[12]
GSM52200
[13]
GSM52201
[14]
GSM52202
[15]
GSM52203
[16]
GSM52204
[17]
GSM52205
[18]
GSM52206
[19]
GSM52207
[20]
GSM52208
[21]
GSM52209
[22]
GSM52210
[23]
GSM52211
[24]
GSM52212
[25]
GSM52213
[26]
GSM52214
[27]
GSM52215
[28]
GSM52216
[29]
GSM52217
[30]
GSM52218
[31]
GSM52219
[32]
GSM52220
[33]
GSM52221
[34]
GSM52222
[35]
GSM52223
[36]
GSM52224
[37]
GSM52225
[38]
GSM52226
[39]
GSM52227
[40]
GSM52228
[41]
GSM52229
[42]
GSM52230
[43]
GSM52231
[44]
GSM52232
[45]
GSM52233
[46]
GSM52234
[47]
GSM52235
[48]
GSM52236
[49]
GSM52237
[50]
GSM52238
[51]
GSM52239
[52]
GSM52240
[53]
GSM52241
[54]
GSM52242
[55]
GSM52243
[56]
GSM52244
[57]
GSM52245
[58]
GSM52246
[59]
GSM52247
[60]
GSM52248
[61]
GSM52249
[62]
GSM52250
[63]
GSM52251
[64]
GSM52252
[65]
GSM52253
[66]
GSM52254
[67]
GSM52255
[68]
GSM52256
[69]
GSM52257
[70]
GSM52258
[71]
GSM52259
[72]
GSM52260
[73]
GSM52261
[74]
GSM52262
[75]
GSM52263
[76]
GSM52264
[77]
GSM52265
[78]
GSM52266
[79]
GSM52267
[80]
GSM52268
[81]
GSM52269
[82]
GSM52270
[83]
GSM52271
[84]
GSM52272
[85]
GSM52273
[86]
GSM52274
[87]
GSM52275
[88]
GSM52276
[89]
GSM52277
[90]
GSM52278
[91]
GSM52279
[92]
GSM52280
[93]
GSM52281
[94]
GSM52282
[95]
GSM52283
[96]
GSM52284
[97]
GSM52285
[98]
GSM52286
[99]
GSM52287
[100]
GSM52288
[101]
GSM52289
[102]
GSM52290
[103]
GSM52291
[104]
GSM52292
[105]
GSM52293
[106]
GSM52294
[107]
GSM52295
[108]
GSM52296
[109]
GSM52297
[110]
GSM52298
[111]
GSM52299
[112]
GSM52300
[113]
GSM52301
[114]
GSM52302
[115]
GSM52303
[116]
GSM52304
[117]
GSM52305
[118]
GSM52306
[119]
GSM52307
[120]
GSM52308
[121]
GSM52309
[122]
GSM52310
[123]
GSM52311
[124]
GSM52312
[125]
GSM52313
sample_count
126
group_sizes
null
group_sizes_basis
null
platform
2121;2118;2116;2119;2120;2117
taxon
Homo sapiens
title
Gastric Cancer Study GC_126
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE2701 not downloaded
[1]
asset:data:geo:GSE2701 licence not read
analysis object · 4 fields
state
partial
methods array · 4 items
[0] object · 10 fields
id
method-1
family
contingency_analysis
specific
chi_square
label
Categorical (contingency table) analysis
dsl_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
categorical_cross_tabulation
evidence object · 3 fields
score
1
band
verbatim
quote
The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test.
[1] object · 10 fields
id
method-2
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Kaplan-Meier
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
cox_proportional_hazards
label
Survival analysis
dsl_operations array · 1 item
[0]
cox_ph
missing_operations array · 0 items
parameters object · 1 field
hazard_ratio
poor overall survival (HR, 0
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.7
band
medium
quote
Cox regression
[3] object · 10 fields
id
method-4
family
survival_analysis
specific
log_rank_test
label
Survival analysis
dsl_operations array · 1 item
[0]
logrank_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
log-rank
targets array · 0 items
gaps array · 1 item
[0]
method.reader_differs_from_extractor
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
chi_square_test
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square.
capability object · 4 fields
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 object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE2701
resolved_accessions array · 1 item
[0]
GSE2701
statements array · 1 item
[0]
Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).
basis
The paper names GSE2701 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
chi_square_test
assets array · 2 items
[0]
source:pmid:27672238
[1]
data:geo:GSE2701
steps array · 1 item
[0]
run_analysis
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
[0]
data:geo:GSE2701
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-10-31T18:29:26Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
null
calls
8
usage object · 3 fields
prompt_tokens
39450
completion_tokens
3066
cached_tokens
2080
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:27672238
type
paper
label
pmid:27672238
[1] object · 3 fields
id
source:pmid:27672238
type
manuscript
label
PMID 27672238 full text
[2] object · 3 fields
id
data:geo:GSE2701
type
dataset
label
GEO GSE2701
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:27672238
type
paper
label
pmid:27672238
[1] object · 3 fields
id
source:pmid:27672238
type
manuscript
label
PMID 27672238 full text
[2] object · 3 fields
id
data:geo:GSE2701
type
dataset
label
GEO GSE2701
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-27672238
type
extraction
used array · 1 item
[0]
source:pmid:27672238
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE2701
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE2701
agent
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:27672238
parent_hash
sha256:4e69a5d8f771244da45436779aaee30528ca9f12413ea141193b9ad8159dd681
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE2701 licence not read
[1]
asset:data:geo:GSE2701 not downloaded
[2]
execution.not_run
[3]
method.reader_differs_from_extractor
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 3 items
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
ssion was analyzed in gastric cancer using a microarray dataset (GSE2701) from the Gene Expression O
[1]
alysis of TBL1XR1 was performed on GC tissue microarray (TMA) to assess its prognostic and biologica
order_basis
paper_text_order:292
id
assay:1
[1] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 4 items
[0]
701) from the Gene Expression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on G
[1]
ression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on GC tis
[2]
ts of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues. 204 of 334 (60.1
[3]
thods 2.2. Patients and Tissue Specimens For immunohistochemistry study, paraffin-embedded pathological specim
order_basis
paper_text_order:361
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
contingency_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
chi_square_test
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test.
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27672238", "kind": "science-record", "revision": 7, "content_hash": "sha256:b89eecb980cbdc8612ef1a4ec4d9f387c694bf7c8ba8b75509caba8786aa13ef", "created_at": "2026-11-01T15:40:20Z", "updated_at": "2026-11-01T21:20:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "TBL1XR1 Is Highly Expressed in Gastric Cancer and Predicts Poor Prognosis.", "doi": "10.1155/2016/2436518", "pmid": "27672238", "authors": ["Fang Liu", "Yuan He", "Qinghua Cao", "Ni Liu", "Wenhui Zhang"], "journal": "Disease markers", "year": 2016, "abstract": "Objective. To investigate the expression of transducin- (β-) like 1 X-linked receptor 1 (TBL1XR1) in human gastric cancer (GC) and its correlation with prognostic and biologic significance. Methods. TBL1XR1 mRNA expression was analyzed in gastric cancer using a microarray dataset (GSE2701) from the Gene Expression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on GC tissue microarray (TMA) to assess its prognostic and biological significance in 334 patients of GC. Results. Analysis of GSE2701 showed that the mRNA levels of TBL1XR1 were significantly elevated in primary gastric tumor and lymph node tissues than normal gastric tissues (P < 0.05). The same results of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues. 204 of 334 (60.1%) primary gastric cancer tissues showed high expression of TBL1XR1 protein. TBL1XR1 overexpression was significantly correlated with lymph node metastasis (P = 0.000) and advanced TNM stage (P = 0.001). Moreover, high levels of TBL1XR1 predicted worse overall survival (P = 0.015). Multivariate Cox regression analysis indicated that high expression of TBL1XR1 was an independent prognostic factor for poor overall survival (HR, 0.525; 95% confidence interval, 0.367-0.752; P = 0.005). Conclusion. This present study demonstrates that TBL1XR1 is overexpressed in gastric cancer and may be a potential predictor and therapeutic target for GC patients.", "claims": [{"id": "claim-method", "statement": "The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672238", "locator": "sections[7] \"2.5. Statistical Analysis\" paragraph 2", "quote": "The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672238", "locator": "sections[3] \"2.1. Gene Expression Profile Data of GSE2701\" paragraph 2", "quote": "Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TBL1XR1 was overexpressed in gastric cancer, and its overexpression was associated with lymph node metastasis, advanced TNM stage, and poor overall survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27672238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Analysis of GSE2701 showed that the mRNA levels of TBL1XR1 were significantly elevated in primary gastric tumor and lymph node tissues than normal gastric tissues (P < 0.05)."}, {"asset": "source:pmid:27672238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The same results of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues."}, {"asset": "source:pmid:27672238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "TBL1XR1 overexpression was significantly correlated with lymph node metastasis (P = 0.000) and advanced TNM stage (P = 0.001)."}, {"asset": "source:pmid:27672238", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Moreover, high levels of TBL1XR1 predicted worse overall survival (P = 0.015)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TBL1XR1 was overexpressed in gastric cancer, and its overexpression was associated with lymph node metastasis, advanced TNM stage, and poor overall survival.", "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:27672238"], "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:GSE2701"], "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:GSE2701"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27672238", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2016/2436518", "sha256": "sha256:7149c699cd03b135e1948ad9f1cc1de05c46bd83e90a9f7e2f36a144e2039761", "bytes": 17953, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2016/2436518", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5031846", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE2701", "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=GSE2701", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2701", "version": null, "note": "Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM52188", "GSM52189", "GSM52190", "GSM52191", "GSM52192", "GSM52193", "GSM52194", "GSM52195", "GSM52196", "GSM52197", "GSM52198", "GSM52199", "GSM52200", "GSM52201", "GSM52202", "GSM52203", "GSM52204", "GSM52205", "GSM52206", "GSM52207", "GSM52208", "GSM52209", "GSM52210", "GSM52211", "GSM52212", "GSM52213", "GSM52214", "GSM52215", "GSM52216", "GSM52217", "GSM52218", "GSM52219", "GSM52220", "GSM52221", "GSM52222", "GSM52223", "GSM52224", "GSM52225", "GSM52226", "GSM52227", "GSM52228", "GSM52229", "GSM52230", "GSM52231", "GSM52232", "GSM52233", "GSM52234", "GSM52235", "GSM52236", "GSM52237", "GSM52238", "GSM52239", "GSM52240", "GSM52241", "GSM52242", "GSM52243", "GSM52244", "GSM52245", "GSM52246", "GSM52247", "GSM52248", "GSM52249", "GSM52250", "GSM52251", "GSM52252", "GSM52253", "GSM52254", "GSM52255", "GSM52256", "GSM52257", "GSM52258", "GSM52259", "GSM52260", "GSM52261", "GSM52262", "GSM52263", "GSM52264", "GSM52265", "GSM52266", "GSM52267", "GSM52268", "GSM52269", "GSM52270", "GSM52271", "GSM52272", "GSM52273", "GSM52274", "GSM52275", "GSM52276", "GSM52277", "GSM52278", "GSM52279", "GSM52280", "GSM52281", "GSM52282", "GSM52283", "GSM52284", "GSM52285", "GSM52286", "GSM52287", "GSM52288", "GSM52289", "GSM52290", "GSM52291", "GSM52292", "GSM52293", "GSM52294", "GSM52295", "GSM52296", "GSM52297", "GSM52298", "GSM52299", "GSM52300", "GSM52301", "GSM52302", "GSM52303", "GSM52304", "GSM52305", "GSM52306", "GSM52307", "GSM52308", "GSM52309", "GSM52310", "GSM52311", "GSM52312", "GSM52313"], "sample_count": 126, "group_sizes": null, "group_sizes_basis": null, "platform": "2121;2118;2116;2119;2120;2117", "taxon": "Homo sapiens", "title": "Gastric Cancer Study GC_126", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE2701 not downloaded", "asset:data:geo:GSE2701 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test."}}, {"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": 0.8, "band": "high", "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": {"hazard_ratio": "poor overall survival (HR, 0"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "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.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "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": ["GSE2701"], "resolved_accessions": ["GSE2701"], "statements": ["Gene expression profile data GSE2701 was downloaded from the open Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) and analyzed by the Qlucore Omics Explorer (QOE 3.1) bioinformatics software (http://www.qlucore.com/)."], "basis": "The paper names GSE2701 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": ["chi_square_test"], "assets": ["source:pmid:27672238", "data:geo:GSE2701"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE2701"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:29:26Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 39450, "completion_tokens": 3066, "cached_tokens": 2080}}, "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:27672238", "type": "paper", "label": "pmid:27672238"}, {"id": "source:pmid:27672238", "type": "manuscript", "label": "PMID 27672238 full text"}, {"id": "data:geo:GSE2701", "type": "dataset", "label": "GEO GSE2701"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27672238", "type": "paper", "label": "pmid:27672238"}, {"id": "source:pmid:27672238", "type": "manuscript", "label": "PMID 27672238 full text"}, {"id": "data:geo:GSE2701", "type": "dataset", "label": "GEO GSE2701"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27672238", "type": "extraction", "used": ["source:pmid:27672238"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE2701", "type": "accession_resolution", "used": ["data:geo:GSE2701"], "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:27672238", "parent_hash": "sha256:4e69a5d8f771244da45436779aaee30528ca9f12413ea141193b9ad8159dd681", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE2701 licence not read", "asset:data:geo:GSE2701 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ssion was analyzed in gastric cancer using a microarray dataset (GSE2701) from the Gene Expression O", "alysis of TBL1XR1 was performed on GC tissue microarray (TMA) to assess its prognostic and biologica"], "order_basis": "paper_text_order:292", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["701) from the Gene Expression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on G", "ression Omnibus (GEO). Immunohistochemistry (IHC) analysis of TBL1XR1 was performed on GC tis", "ts of TBL1XR1 protein level were observed by IHC staining in 334 GC tissues. 204 of 334 (60.1", "thods 2.2. Patients and Tissue Specimens For immunohistochemistry study, paraffin-embedded pathological specim"], "order_basis": "paper_text_order:361", "id": "assay:2"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The associations between TBL1XR1 expression and clinicopathological features were analyzed by chi-square (χ 2) test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}