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

pmid:38941002

FUT11 expression in gastric cancer: its prognostic significance and role in immune regulation.

Yanqing Huang · Xiaoying Yang · Mengda Wei · Xi Yang · Zhenmin Yuan · Junjie Huang · Junren Wei · Lei Tian

Discover oncology · 2024 doi:10.1007/s12672-024-01120-y

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:38941002
kind
science-record
content_hash
sha256:5618354ee3087afe1a95660868569d15e24ad142273b5e618f818b5d04d3973b
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:29:01Z
updated_at
2026-11-01T22:12:09Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
FUT11 expression in gastric cancer: its prognostic significance and role in immune regulation.
doi
10.1007/s12672-024-01120-y
pmid
38941002
authors array · 8 items
[0]
Yanqing Huang
[1]
Xiaoying Yang
[2]
Mengda Wei
[3]
Xi Yang
[4]
Zhenmin Yuan
[5]
Junjie Huang
[6]
Junren Wei
[7]
Lei Tian
journal
Discover oncology
year
2024
abstract
BACKGROUND: Gastric cancer (GC) is a malignant digestive tract tumor with a high recurrence rate and poor prognosis. Fucosylation is important in tumor glycosylation, in which the key enzyme is fucosyltransferase (FUT). FUT11 is a member of the fucosyltransferase family and has been closely associated with the development of multiple cancers. However, the specific relationship between FUT11 and GC prognosis and its molecular mechanism has not been fully studied. This study explored FUT11 expression, clinical correlation, and its role in GC occurrence and development to deepen understanding of its function. METHODS: FUT11 expression in 33 cancers was preliminarily analyzed using the Tumor Immunoassay Resource (TIMER2.0) database. FUT11 expression in GC was evaluated using The Cancer Genome Atlas stomach adenocarcinoma (TCGA-STAD) and Gene Expression Profiling Interactive Analysis (GEPIA2) data and verified using the Gene Expression Omnibus (GEO) GSE65801 dataset. Furthermore, we studied the survival prognosis of FUT11 in GC and analyzed its effect on the survival rate of patients with GC using the KM-plotter. We also performed COX regression analysis on TCGA GC clinical data and analyzed FUT11 expression in the pathway using the STRING and LinkedOmics databases. Moreover, the relationship between FUT11 and GC immune infiltration level was examined, and the Kaplan-Meier survival analysis diagram was constructed. The FUT11 genetic variation information was retrieved using cBioPortal, and its drug sensitivity was analyzed using CellMiner. Finally, differential FUT11 expression in GC tissues was verified using immunohistochemistry. RESULTS: The data mining and analysis demonstrated that FUT11 expression was abnormally elevated in GC tissues and correlated with poor patient prognosis. The FUT11 expression level was an independent prognostic factor for GC. The difference in FUT11 expression level resulted in different degrees of immune cell infiltration in the patients with GC, which might regulate the tumor microenvironment. FUT11 affected GC development by participating in cancer pathways such as PI3K-AKT, neuroactive ligand-receptor, and MAPK. Immunohistochemical staining revealed that FUT11 was highly expressed in GC. CONCLUSIONS: This study revealed that FUT11 expression is significantly increased in GC tissues. This increase is associated with poor prognosis and might affect immune regulation. FUT11 might have immunological and targeted therapeutic value, providing a new approach to GC treatment.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38941002
locator
sections[5] "Clinical data analysis of FUT11 in patients with GC" paragraph 3
quote
Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:38941002
locator
sections[30] "notes" paragraph 1
quote
The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
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:38941002
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:GSE65801
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:GSE65801
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:38941002
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s12672-024-01120-y
sha256
sha256:fbfaac8cd920bc3d491dbf755bc6d2c808035e6ad218fa515be055c8af7f32a0
bytes
51925
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s12672-024-01120-y
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
PMC11213843
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE65801
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=GSE65801
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE65801
version
null
note
The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.
access_statement_kind
data_availability_statement
sample_accessions array · 64 items
[0]
GSM1606492
[1]
GSM1606493
[2]
GSM1606494
[3]
GSM1606495
[4]
GSM1606496
[5]
GSM1606497
[6]
GSM1606498
[7]
GSM1606499
[8]
GSM1606500
[9]
GSM1606501
[10]
GSM1606502
[11]
GSM1606503
[12]
GSM1606504
[13]
GSM1606505
[14]
GSM1606506
[15]
GSM1606507
[16]
GSM1606508
[17]
GSM1606509
[18]
GSM1606510
[19]
GSM1606511
[20]
GSM1606512
[21]
GSM1606513
[22]
GSM1606514
[23]
GSM1606515
[24]
GSM1606516
[25]
GSM1606517
[26]
GSM1606518
[27]
GSM1606519
[28]
GSM1606520
[29]
GSM1606521
[30]
GSM1606522
[31]
GSM1606523
[32]
GSM1606524
[33]
GSM1606525
[34]
GSM1606526
[35]
GSM1606527
[36]
GSM1606528
[37]
GSM1606529
[38]
GSM1606530
[39]
GSM1606531
[40]
GSM1606532
[41]
GSM1606533
[42]
GSM1606534
[43]
GSM1606535
[44]
GSM1606536
[45]
GSM1606537
[46]
GSM1606538
[47]
GSM1606539
[48]
GSM1606540
[49]
GSM1606541
[50]
GSM1606542
[51]
GSM1606543
[52]
GSM1606544
[53]
GSM1606545
[54]
GSM1606546
[55]
GSM1606547
[56]
GSM1606548
[57]
GSM1606549
[58]
GSM1606550
[59]
GSM1606551
[60]
GSM1606552
[61]
GSM1606553
[62]
GSM1606554
[63]
GSM1606555
sample_count
64
group_sizes
null
group_sizes_basis
null
platform
14550
taxon
Homo sapiens
title
Characterization of differentially expressed genes involved in pathways associated with gastric cancer
resolution_checked_at
2026-11-01T15:39:55Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE65801 not downloaded
[1]
asset:data:geo:GSE65801 licence not read
analysis object · 4 fields
state
partial
methods array · 10 items
[0] object · 10 fields
id
method-1
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 · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
1
band
verbatim
quote
Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC.
[1] object · 10 fields
id
method-2
family
group_comparison
specific
wilcoxon
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
group_comparison_wilcoxon
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
Wilcoxon
[2] object · 10 fields
id
method-3
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
0.7
band
medium
quote
KM
[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 · 1 field
hazard_ratio
lues and hazard ratios (HR) for 95% confidence int
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Log-rank
[4] object · 10 fields
id
method-5
family
correlation_analysis
specific
spearman
label
Correlation analysis
dsl_operations array · 1 item
[0]
spearman_rho
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
paired_numeric_columns
evidence object · 3 fields
score
0.8
band
high
quote
Spearman correlation
[5] object · 10 fields
id
method-6
family
network_analysis
specific
ppi_network
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.8
band
high
quote
PPI
[6] object · 10 fields
id
method-7
family
network_analysis
specific
pathway_enrichment
label
Network / pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.8
band
high
quote
pathway enrichment
[7] object · 10 fields
id
method-8
family
network_analysis
specific
centrality
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.8
band
high
quote
centrality
[8] object · 10 fields
id
method-9
family
diagnostic_evaluation
specific
roc
label
Diagnostic test evaluation
dsl_operations array · 6 items
[0]
confusion_counts
[1]
roc_curve
[2]
sensitivity_specificity
[3]
solve_confusion_matrix
[4]
classification_metrics
[5]
published_precision_envelope
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
reference_standard_and_test
evidence object · 3 fields
score
0.8
band
high
quote
ROC curve
[9] object · 10 fields
id
method-10
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
0.8
band
high
quote
χ2
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]
cox_ph
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: cox_proportional_hazards.
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]
GSE65801
resolved_accessions array · 1 item
[0]
GSE65801
statements array · 1 item
[0]
The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.
basis
The paper names GSE65801 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]
cox_ph
assets array · 2 items
[0]
source:pmid:38941002
[1]
data:geo:GSE65801
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:GSE65801
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
2026-11-01T19:22:48Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
13741
completion_tokens
3172
cached_tokens
264
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:38941002
type
paper
label
pmid:38941002
[1] object · 3 fields
id
source:pmid:38941002
type
manuscript
label
PMID 38941002 full text
[2] object · 3 fields
id
data:geo:GSE65801
type
dataset
label
GEO GSE65801
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:38941002
type
paper
label
pmid:38941002
[1] object · 3 fields
id
source:pmid:38941002
type
manuscript
label
PMID 38941002 full text
[2] object · 3 fields
id
data:geo:GSE65801
type
dataset
label
GEO GSE65801
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-38941002
type
extraction
used array · 1 item
[0]
source:pmid:38941002
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE65801
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE65801
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:38941002
parent_hash
sha256:840844c5a3287a89d0a3e51c5d8e362a442571a6e66501040930fc1d3f8fb0e9
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE65801 licence not read
[1]
asset:data:geo:GSE65801 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 · 4 items
[0] 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 · 2 items
[0]
expression in GC tissues was verified using immunohistochemistry. RESULTS: The data mining and analysis demon
[1]
-AKT, neuroactive ligand-receptor, and MAPK. Immunohistochemical staining revealed that FUT11 was highly expr
order_basis
paper_text_order:1684
id
assay:1
[1] 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
0.93
evidence array · 1 item
[0]
descent, while Gene Expression Omnibus (GEO) microarray data is predominantly from Chinese populatio
order_basis
paper_text_order:3663
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
rna_seq
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 3 items
[0]
the standardized analysis of RNA sequencing (RNA-seq) data of 9736 tumor samples and 8587 normal
[1]
tool that aided the standardized analysis of RNA sequencing (RNA-seq) data of 9736 tumor samples and 858
[2]
A), and TCGA public gene chip databases, and RNA-seq was constructed from the data. KM-plotter wa
order_basis
paper_text_order:4059
id
assay:3
[3] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
cox_ph
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC.
order_basis
consumes_earlier_output
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38941002", "kind": "science-record", "revision": 3, "content_hash": "sha256:5618354ee3087afe1a95660868569d15e24ad142273b5e618f818b5d04d3973b", "created_at": "2026-11-01T20:29:01Z", "updated_at": "2026-11-01T22:12:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FUT11 expression in gastric cancer: its prognostic significance and role in immune regulation.", "doi": "10.1007/s12672-024-01120-y", "pmid": "38941002", "authors": ["Yanqing Huang", "Xiaoying Yang", "Mengda Wei", "Xi Yang", "Zhenmin Yuan", "Junjie Huang", "Junren Wei", "Lei Tian"], "journal": "Discover oncology", "year": 2024, "abstract": "BACKGROUND: Gastric cancer (GC) is a malignant digestive tract tumor with a high recurrence rate and poor prognosis. Fucosylation is important in tumor glycosylation, in which the key enzyme is fucosyltransferase (FUT). FUT11 is a member of the fucosyltransferase family and has been closely associated with the development of multiple cancers. However, the specific relationship between FUT11 and GC prognosis and its molecular mechanism has not been fully studied. This study explored FUT11 expression, clinical correlation, and its role in GC occurrence and development to deepen understanding of its function.\nMETHODS: FUT11 expression in 33 cancers was preliminarily analyzed using the Tumor Immunoassay Resource (TIMER2.0) database. FUT11 expression in GC was evaluated using The Cancer Genome Atlas stomach adenocarcinoma (TCGA-STAD) and Gene Expression Profiling Interactive Analysis (GEPIA2) data and verified using the Gene Expression Omnibus (GEO) GSE65801 dataset. Furthermore, we studied the survival prognosis of FUT11 in GC and analyzed its effect on the survival rate of patients with GC using the KM-plotter. We also performed COX regression analysis on TCGA GC clinical data and analyzed FUT11 expression in the pathway using the STRING and LinkedOmics databases. Moreover, the relationship between FUT11 and GC immune infiltration level was examined, and the Kaplan-Meier survival analysis diagram was constructed. The FUT11 genetic variation information was retrieved using cBioPortal, and its drug sensitivity was analyzed using CellMiner. Finally, differential FUT11 expression in GC tissues was verified using immunohistochemistry.\nRESULTS: The data mining and analysis demonstrated that FUT11 expression was abnormally elevated in GC tissues and correlated with poor patient prognosis. The FUT11 expression level was an independent prognostic factor for GC. The difference in FUT11 expression level resulted in different degrees of immune cell infiltration in the patients with GC, which might regulate the tumor microenvironment. FUT11 affected GC development by participating in cancer pathways such as PI3K-AKT, neuroactive ligand-receptor, and MAPK. Immunohistochemical staining revealed that FUT11 was highly expressed in GC.\nCONCLUSIONS: This study revealed that FUT11 expression is significantly increased in GC tissues. This increase is associated with poor prognosis and might affect immune regulation. FUT11 might have immunological and targeted therapeutic value, providing a new approach to GC treatment.", "claims": [{"id": "claim-method", "statement": "Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38941002", "locator": "sections[5] \"Clinical data analysis of FUT11 in patients with GC\" paragraph 3", "quote": "Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38941002", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:38941002"], "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:GSE65801"], "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:GSE65801"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38941002", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-024-01120-y", "sha256": "sha256:fbfaac8cd920bc3d491dbf755bc6d2c808035e6ad218fa515be055c8af7f32a0", "bytes": 51925, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-024-01120-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11213843", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65801", "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=GSE65801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65801", "version": null, "note": "The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1606492", "GSM1606493", "GSM1606494", "GSM1606495", "GSM1606496", "GSM1606497", "GSM1606498", "GSM1606499", "GSM1606500", "GSM1606501", "GSM1606502", "GSM1606503", "GSM1606504", "GSM1606505", "GSM1606506", "GSM1606507", "GSM1606508", "GSM1606509", "GSM1606510", "GSM1606511", "GSM1606512", "GSM1606513", "GSM1606514", "GSM1606515", "GSM1606516", "GSM1606517", "GSM1606518", "GSM1606519", "GSM1606520", "GSM1606521", "GSM1606522", "GSM1606523", "GSM1606524", "GSM1606525", "GSM1606526", "GSM1606527", "GSM1606528", "GSM1606529", "GSM1606530", "GSM1606531", "GSM1606532", "GSM1606533", "GSM1606534", "GSM1606535", "GSM1606536", "GSM1606537", "GSM1606538", "GSM1606539", "GSM1606540", "GSM1606541", "GSM1606542", "GSM1606543", "GSM1606544", "GSM1606545", "GSM1606546", "GSM1606547", "GSM1606548", "GSM1606549", "GSM1606550", "GSM1606551", "GSM1606552", "GSM1606553", "GSM1606554", "GSM1606555"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "14550", "taxon": "Homo sapiens", "title": "Characterization of differentially expressed genes involved in pathways associated with gastric cancer", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE65801 not downloaded", "asset:data:geo:GSE65801 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "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": "KM"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "lues and hazard ratios (HR) for 95% confidence int"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Log-rank"}}, {"id": "method-5", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-6", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-7", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-8", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "centrality"}}, {"id": "method-9", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-10", "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": "χ2"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65801"], "resolved_accessions": ["GSE65801"], "statements": ["The standardized datasets involved in this study were sourced from the TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo/) databases, and all data were from different biological samples, without considering repeated testing.The data and materials that support the findings of this study are available on request from Discover Oncology."], "basis": "The paper names GSE65801 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:38941002", "data:geo:GSE65801"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65801"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:22:48Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13741, "completion_tokens": 3172, "cached_tokens": 264}}, "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:38941002", "type": "paper", "label": "pmid:38941002"}, {"id": "source:pmid:38941002", "type": "manuscript", "label": "PMID 38941002 full text"}, {"id": "data:geo:GSE65801", "type": "dataset", "label": "GEO GSE65801"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38941002", "type": "paper", "label": "pmid:38941002"}, {"id": "source:pmid:38941002", "type": "manuscript", "label": "PMID 38941002 full text"}, {"id": "data:geo:GSE65801", "type": "dataset", "label": "GEO GSE65801"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38941002", "type": "extraction", "used": ["source:pmid:38941002"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65801", "type": "accession_resolution", "used": ["data:geo:GSE65801"], "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:38941002", "parent_hash": "sha256:840844c5a3287a89d0a3e51c5d8e362a442571a6e66501040930fc1d3f8fb0e9", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE65801 licence not read", "asset:data:geo:GSE65801 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["expression in GC tissues was verified using immunohistochemistry. RESULTS: The data mining and analysis demon", "-AKT, neuroactive ligand-receptor, and MAPK. Immunohistochemical staining revealed that FUT11 was highly expr"], "order_basis": "paper_text_order:1684", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["descent, while Gene Expression Omnibus (GEO) microarray data is predominantly from Chinese populatio"], "order_basis": "paper_text_order:3663", "id": "assay:2"}, {"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": ["the standardized analysis of RNA sequencing (RNA-seq) data of 9736 tumor samples and 8587 normal", "tool that aided the standardized analysis of RNA sequencing (RNA-seq) data of 9736 tumor samples and 858", "A), and TCGA public gene chip databases, and RNA-seq was constructed from the data. KM-plotter wa"], "order_basis": "paper_text_order:4059", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Subsequently, univariate and multivariate COX regression analyses were conducted using the survminer, survival, and rms packages in R language to reveal the relationship between FUT11 expression and the clinical characteristics of patients with GC."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}