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

pmid:28522860

Involvement of FAK-ERK2 signaling pathway in CKAP2-induced proliferation and motility in cervical carcinoma cell lines.

Qi-Sang Guo · Yu Song · Ke-Qin Hua · Shu-Jun Gao

Scientific reports · 2017 doi:10.1038/s41598-017-01832-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:28522860
kind
science-record
content_hash
sha256:20e0060ebe67523d8871916670c03025e88b99ddf6a118d14da6269241f2d366
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:26Z
updated_at
2026-11-01T21:20:55Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Involvement of FAK-ERK2 signaling pathway in CKAP2-induced proliferation and motility in cervical carcinoma cell lines.
doi
10.1038/s41598-017-01832-y
pmid
28522860
authors array · 4 items
[0]
Qi-Sang Guo
[1]
Yu Song
[2]
Ke-Qin Hua
[3]
Shu-Jun Gao
journal
Scientific reports
year
2017
abstract
Cervical carcinoma is the fourth most common cause of death in woman, caused by human papillomavirus (HPV) infections and arising from the cervix. Cytoskeleton-associated protein 2 (CKAP2), also known as tumor-associated microtubule-associated protein, has been linked to tumorigenic effects. In the present study, we screened CKAP2 as a new candidate gene which promotes development of cervical carcinoma, in two independent datasets (TCGA and GSE27678). Results showed that CKAP2 expression was significantly up-regulated in cervical cancerous tissues compared with normal counterparts. Gene set enrichment analysis (GSEA) showed that metastasis, cell cycle and FAK pathways were related with elevated CKAP2 expression. Knockdown of CKAP2 expression significantly inhibited cell proliferation, migration and invasion both in HeLa and C-33A cells. And depletion of CKAP2 down-regulated the expression of metastasis and cell cycle related proteins as well as the phosphorylation of ERK2 (p-ERK2), except E-cadherin. In vivo experiment revealed that knockdown of CKAP2 inhibited C-33A cells proliferation. However, FAK inhibitor PF-562271 and ERK2 inhibitor VX-11e treatment significantly inhibited CKAP2 overexpression-induced cell proliferation, migration and invasion in SiHa cells. In conclusion, our study suggests that CKAP2 acts as a functional oncogene in cervical carcinoma development and may exert its function by targeting FAK-ERK2 signaling pathway.
claims array · 3 items
[0] object · 6 fields
id
claim-method
statement
To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:28522860
locator
sections[13] "Bioinformatics analysis" paragraph 2
quote
To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:28522860
locator
sections[13] "Bioinformatics analysis" paragraph 2
quote
RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.
state
complete
[2] object · 6 fields
id
claim-target-result
statement
The paper used gene set enrichment analysis (GSEA) on CKAP2 expression in the TCGA and GSE27678 cervical carcinoma datasets; the GSEA identified metastasis-up, cell-cycle, and FAK pathways as associated with elevated CKAP2 expression.
kind
qualitative
target
null
evidence array · 2 items
[0] object · 3 fields
asset
source:pmid:28522860
locator
sections[0] "Abstract" paragraph 1
quote
In the present study, we screened CKAP2 as a new candidate gene which promotes development of cervical carcinoma, in two independent datasets (TCGA and GSE27678).
[1] object · 3 fields
asset
source:pmid:28522860
locator
sections[0] "Abstract" paragraph 1
quote
Gene set enrichment analysis (GSEA) showed that metastasis, cell cycle and FAK pathways were related with elevated CKAP2 expression.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
The paper used gene set enrichment analysis (GSEA) on CKAP2 expression in the TCGA and GSE27678 cervical carcinoma datasets; the GSEA identified metastasis-up, cell-cycle, and FAK pathways as associated with elevated CKAP2 expression.
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:28522860
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:GSE27678
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:GSE27678
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 · 5 items
[0] object · 15 fields
id
source:pmid:28522860
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41598-017-01832-y
sha256
sha256:dbb720b11a3f66cb582cd7319467bce4d2d2c09a9cc38afbbb7f82c73fcea26d
bytes
43190
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41598-017-01832-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
PMC5437009
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE27678
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=GSE27678
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE27678
version
null
note
RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.
access_statement_kind
repository_route_statement
sample_accessions array · 77 items
[0]
GSM685524
[1]
GSM685525
[2]
GSM685526
[3]
GSM685527
[4]
GSM685528
[5]
GSM685529
[6]
GSM685530
[7]
GSM685531
[8]
GSM685532
[9]
GSM685533
[10]
GSM685534
[11]
GSM685535
[12]
GSM685536
[13]
GSM685537
[14]
GSM685538
[15]
GSM685539
[16]
GSM685540
[17]
GSM685541
[18]
GSM685542
[19]
GSM685543
[20]
GSM685544
[21]
GSM685545
[22]
GSM685546
[23]
GSM685547
[24]
GSM685548
[25]
GSM685549
[26]
GSM685550
[27]
GSM685551
[28]
GSM685552
[29]
GSM685553
[30]
GSM685554
[31]
GSM685555
[32]
GSM685556
[33]
GSM685557
[34]
GSM685558
[35]
GSM685559
[36]
GSM685560
[37]
GSM685561
[38]
GSM685562
[39]
GSM685563
[40]
GSM685564
[41]
GSM685565
[42]
GSM685566
[43]
GSM685567
[44]
GSM685568
[45]
GSM685569
[46]
GSM685570
[47]
GSM685571
[48]
GSM685572
[49]
GSM685573
[50]
GSM685574
[51]
GSM685575
[52]
GSM685576
[53]
GSM685577
[54]
GSM685578
[55]
GSM685579
[56]
GSM685580
[57]
GSM685581
[58]
GSM685582
[59]
GSM685583
[60]
GSM685584
[61]
GSM685585
[62]
GSM685586
[63]
GSM685587
[64]
GSM685588
[65]
GSM685589
[66]
GSM685590
[67]
GSM685591
[68]
GSM685592
[69]
GSM685593
[70]
GSM685594
[71]
GSM685595
[72]
GSM685596
[73]
GSM685597
[74]
GSM685598
[75]
GSM685599
[76]
GSM685600
sample_count
77
group_sizes
null
group_sizes_basis
null
platform
570;571
taxon
Homo sapiens
title
Gene expression analysis in a variety of normal, premalignant and squamous cell carcinomas of the cervix
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
[2] object · 16 fields
id
asset:table:pmid:28522860:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:0fb2a87e96926f57e61309835aee3fbafac89e3eba0e314adbfcf61204b92882
bytes
899
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[3]/table-wrap[1]#Tab1
version
null
note
Relationship between CKAP2 and clinical characteristics of cervical carcinoma patients.
structure object · 5 fields
pmcid
PMC5437009
section_index
3
section_title
Tissue samples
row_count
20
column_count
5
table object · 8 fields
label
Table 1
caption
Relationship between CKAP2 and clinical characteristics of cervical carcinoma patients.
rows array · 20 items
[0] array · 4 items
[0]
Factor
[1]
Characteristic
[2]
CKAP2 expression (N)
[3]
P-values
[1] array · 2 items
[0]
Lower
[1]
Higher
[2] array · 5 items
[0]
Age (years)
[1]
<35
[2]
60
[3]
42
[4]
0.023
[3] array · 3 items
[0]
>=35
[1]
62
[2]
83
[4] array · 5 items
[0]
Histology
[1]
Squamous
[2]
105
[3]
110
[4]
0.653
[5] array · 3 items
[0]
Adenocarcinoma
[1]
17
[2]
15
[6] array · 5 items
[0]
HPV
[1]
HPV16
[2]
78
[3]
80
[4]
0.536
[7] array · 3 items
[0]
HPV18
[1]
27
[2]
31
[8] array · 3 items
[0]
Others
[1]
17
[2]
14
[9] array · 5 items
[0]
FIGO stage
[1]
Ib~IIa
[2]
21
[3]
6
[4]
0.005
[10] array · 3 items
[0]
IIb~IIIa
[1]
101
[2]
119
[11] array · 5 items
[0]
Histological differentiation
[1]
Well
[2]
5
[3]
8
[4]
0.521
[12] array · 3 items
[0]
Moderate
[1]
78
[2]
73
[13] array · 3 items
[0]
poor
[1]
39
[2]
44
[14] array · 5 items
[0]
Lymph node metastasis
[1]
Negative
[2]
115
[3]
78
[4]
<0.0001
[15] array · 3 items
[0]
Positive
[1]
7
[2]
47
[16] array · 5 items
[0]
Recurrence
[1]
Yes
[2]
27
[3]
59
[4]
0.002
[17] array · 3 items
[0]
No
[1]
95
[2]
66
[18] array · 5 items
[0]
Tumor maximum diameter (cm)
[1]
<4
[2]
98
[3]
80
[4]
0.006
[19] array · 3 items
[0]
>=4
[1]
24
[2]
45
locator
section[3]/table-wrap[1]#Tab1
[3] object · 16 fields
id
asset:table:pmid:28522860:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:40751c615758ae20705bb3eb5b440f8430c6556271d5aa1c3ecf2c1bb61d7fd7
bytes
938
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[8]/table-wrap[1]#Tab2
version
null
note
Primes sequences used in this study.
structure object · 5 fields
pmcid
PMC5437009
section_index
8
section_title
Reverse transcription-quantitative polymerase chain reaction
row_count
15
column_count
2
table object · 8 fields
label
Table 2
caption
Primes sequences used in this study.
rows array · 15 items
[0] array · 2 items
[0]
Gene
[1]
Sequences
[1] array · 2 items
[0]
CKAP2-forward
[1]
5′-GCCCAAAGAAACCTCGGAAG-3′
[2] array · 2 items
[0]
CKAP2-reverse
[1]
5′-GCAGGCTCATGCTGAGTAAC-3′
[3] array · 2 items
[0]
PCNA-forward
[1]
5′-GGTGTTGGAGGCACTCAAGG-3′
[4] array · 2 items
[0]
PCNA-reverse
[1]
5′-CAGGGTGAGCTGCACCAAAG-3′
[5] array · 2 items
[0]
MMP-2-forward
[1]
5′-TTGACGGTAAGGACGGACTC-3′
[6] array · 2 items
[0]
MMP-2-reverse
[1]
5′-GGCGTTCCCATACTTCACAC-3′
[7] array · 2 items
[0]
MMP-9-forward
[1]
5′-AAGGGCGTCGTGGTTCCAACTC-3′
[8] array · 2 items
[0]
MMP-9-reverse
[1]
5′-AGCATTGCCGTCCTGGGTGTAG-3′
[9] array · 2 items
[0]
Snail -forward
[1]
5′-TTCCTGAGCTGGCCTGTCTG-3′
[10] array · 2 items
[0]
Snail-reverse
[1]
5′-TGGCCTGAGGGTTCCTTGTG-3′
[11] array · 2 items
[0]
E-cadherin-forward
[1]
5′-GAGAACGCATTGCCACATACAC-3′
[12] array · 2 items
[0]
E-cadherin-reverse
[1]
5′-AAGAGCACCTTCCATGACAGAC-3′
[13] array · 2 items
[0]
GAPDH-forward
[1]
5′-CACCCACTCCTCCACCTTTG-3′
[14] array · 2 items
[0]
GAPDH-reverse
[1]
5′-CCACCACCCTGTTGCTGTAG-3′
locator
section[8]/table-wrap[1]#Tab2
[4] object · 16 fields
id
asset:table:pmid:28522860:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:f6e289ecffd6bf0c460205bab6b32cfe70877e03f5ea71e6b55571f9eee3c49d
bytes
1177
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[16]/table-wrap[1]#Tab3
version
null
note
Univariate and multivariate analysis of clinicopathological factors for overall survival.
structure object · 5 fields
pmcid
PMC5437009
section_index
16
section_title
CKAP2 expression is upregulated in human cervical carcinoma tissues
row_count
11
column_count
8
table object · 8 fields
label
Table 3
caption
Univariate and multivariate analysis of clinicopathological factors for overall survival.
rows array · 11 items
[0] array · 4 items
[0]
Clinicopathological
[1]
Subset
[2]
Univariate analysis
[3]
Multivariate analysis
[1] array · 6 items
[0]
HR
[1]
95% CI
[2]
p value
[3]
HR
[4]
95% CI
[5]
p value
[2] array · 8 items
[0]
Age (years)
[1]
<35 vs. >=35
[2]
1.116
[3]
0.628–2.121
[4]
0.589
[5]
[6]
[7]
[3] array · 8 items
[0]
Histology
[1]
Squamous vs. Adenocarcinoma
[2]
1.128
[3]
0.477–2.691
[4]
0.748
[5]
[6]
[7]
[4] array · 8 items
[0]
HPV
[1]
HPV16, HPV18 vs. Others
[2]
1.498
[3]
0.774–2.987
[4]
0.231
[5]
[6]
[7]
[5] array · 8 items
[0]
FIGO stage
[1]
Ib~IIa vs. IIb~IIIa
[2]
3.618
[3]
1.935–6.984
[4]
<0.0001
[5]
2.318
[6]
1.157–4.646
[7]
0.018
[6] array · 8 items
[0]
Histological differentiation
[1]
Well vs. moderate, poor
[2]
0.725
[3]
0.400–1.382
[4]
0.472
[5]
[6]
[7]
[7] array · 8 items
[0]
Lymph node metastasis
[1]
Positive vs. negative
[2]
4.253
[3]
2.424–8.308
[4]
<0.0001
[5]
2.236
[6]
1.144–4.926
[7]
0.005
[8] array · 8 items
[0]
Recurrence
[1]
Yes vs. No
[2]
1.708
[3]
0.802–3.813
[4]
0.139
[5]
[6]
[7]
[9] array · 8 items
[0]
Tumor maximum diameter (cm)
[1]
<4 vs. >=4
[2]
1.374
[3]
0.624–2.491
[4]
0.539
[5]
[6]
[7]
[10] array · 8 items
[0]
CKAP2 expression
[1]
High vs. Low
[2]
4.686
[3]
2.175–9.882
[4]
<0.0001
[5]
2.383
[6]
1.234–6.481
[7]
0.013
locator
section[16]/table-wrap[1]#Tab3
gaps array · 2 items
[0]
asset:data:geo:GSE27678 not downloaded
[1]
asset:data:geo:GSE27678 licence not read
analysis object · 4 fields
state
partial
methods array · 5 items
[0] object · 10 fields
id
method-1
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
[1] object · 10 fields
id
method-2
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 · 2 fields
hazard_ratio
formed to calculate the hazard ratio (HR) and the 95% confid
confidence_interval
ratio (HR) and the 95% confidence interval (CI) to evaluate the as
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Cox proportional hazards
[2] object · 10 fields
id
method-3
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
[3] object · 10 fields
id
method-4
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
[4] object · 10 fields
id
method-5
family
null
specific
null
label
Gene set enrichment analysis (GSEA)
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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]
survival_km
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: kaplan_meier.
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]
GSE27678
resolved_accessions array · 1 item
[0]
GSE27678
statements array · 1 item
[0]
RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.
basis
The paper names GSE27678 in NCBI 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]
survival_km
assets array · 5 items
[0]
source:pmid:28522860
[1]
data:geo:GSE27678
[2]
asset:table:pmid:28522860:1
[3]
asset:table:pmid:28522860:2
[4]
asset:table:pmid:28522860:3
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:GSE27678
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
2026-10-31T18:31:08Z
independence
same_provider
evidence_check object · 2 fields
method
verbatim
availability
null
calls
8
usage object · 3 fields
prompt_tokens
92641
completion_tokens
3650
cached_tokens
1824
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:28522860
type
paper
label
pmid:28522860
[1] object · 3 fields
id
source:pmid:28522860
type
manuscript
label
PMID 28522860 full text
[2] object · 3 fields
id
data:geo:GSE27678
type
dataset
label
GEO GSE27678
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:28522860
type
paper
label
pmid:28522860
[1] object · 3 fields
id
source:pmid:28522860
type
manuscript
label
PMID 28522860 full text
[2] object · 3 fields
id
data:geo:GSE27678
type
dataset
label
GEO GSE27678
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-28522860
type
extraction
used array · 1 item
[0]
source:pmid:28522860
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE27678
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE27678
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:28522860
parent_hash
sha256:57e211cb31059b7670d69242917a99d42928fc41c6fc5092bec2221dccfb525e
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE27678 licence not read
[1]
asset:data:geo:GSE27678 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 6 items
[0] object · 11 fields
role
data_generation
definition_id
transfection
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]
were related with elevated CKAP2 expression. Knockdown of CKAP2 expression significantly inhibited
[1]
E-cadherin. In vivo experiment revealed that knockdown of CKAP2 inhibited C-33A cells proliferation
[2]
C-33A cells infected with pLKO.1-EGFP-CKAP2 shRNA compared with controls as well as the expres
[3]
s increased in response to pLKO.1-EGFP-CKAP2 shRNA infection. The similar results were also fou
order_basis
paper_text_order:797
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
cell_culture
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]
roliferation, migration and invasion both in HeLa and C-33A cells. And depletion of CKAP2 down
[1]
were used in this study. All the cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hy
[2]
cervical carcinoma cell lines (C-33A, CaSki, HeLa, SiHa and C4-1) obtained from the Cell Bank
[3]
9 and Snail) were significantly decreased in HeLa and C-33A cells infected with pLKO.1-EGFP-CK
order_basis
paper_text_order:902
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
animal_model
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.77
evidence array · 1 item
[0]
ylation of ERK2 (p-ERK2), except E-cadherin. In vivo experiment revealed that knockdown of CKAP2
order_basis
paper_text_order:1091
id
assay:3
[3] 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]
o validate the results in GSEA, we performed Real-time PCR and Western blot analysis in cervical carcin
[1]
MMP-9, Snail and E-cadherin was analyzed by Real-time PCR (A,B) and Western blot (C,D). ***P < 0.001.
order_basis
paper_text_order:4263
id
assay:4
[4] object · 11 fields
role
data_generation
definition_id
western_blot
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]
ults in GSEA, we performed Real-time PCR and Western blot analysis in cervical carcinoma cells. As sho
[1]
. The similar results were also found in our Western blot analysis in both HeLa and C-33A cells (Fig.
[2]
erin was analyzed by Real-time PCR (A,B) and Western blot (C,D). ***P < 0.001. Electronic supplementar
order_basis
paper_text_order:4281
id
assay:5
[5] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
[0]
survival_km
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
Kaplan-Meier
order_basis
consumes_earlier_output
id
assay:6
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28522860", "kind": "science-record", "revision": 7, "content_hash": "sha256:20e0060ebe67523d8871916670c03025e88b99ddf6a118d14da6269241f2d366", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Involvement of FAK-ERK2 signaling pathway in CKAP2-induced proliferation and motility in cervical carcinoma cell lines.", "doi": "10.1038/s41598-017-01832-y", "pmid": "28522860", "authors": ["Qi-Sang Guo", "Yu Song", "Ke-Qin Hua", "Shu-Jun Gao"], "journal": "Scientific reports", "year": 2017, "abstract": "Cervical carcinoma is the fourth most common cause of death in woman, caused by human papillomavirus (HPV) infections and arising from the cervix. Cytoskeleton-associated protein 2 (CKAP2), also known as tumor-associated microtubule-associated protein, has been linked to tumorigenic effects. In the present study, we screened CKAP2 as a new candidate gene which promotes development of cervical carcinoma, in two independent datasets (TCGA and GSE27678). Results showed that CKAP2 expression was significantly up-regulated in cervical cancerous tissues compared with normal counterparts. Gene set enrichment analysis (GSEA) showed that metastasis, cell cycle and FAK pathways were related with elevated CKAP2 expression. Knockdown of CKAP2 expression significantly inhibited cell proliferation, migration and invasion both in HeLa and C-33A cells. And depletion of CKAP2 down-regulated the expression of metastasis and cell cycle related proteins as well as the phosphorylation of ERK2 (p-ERK2), except E-cadherin. In vivo experiment revealed that knockdown of CKAP2 inhibited C-33A cells proliferation. However, FAK inhibitor PF-562271 and ERK2 inhibitor VX-11e treatment significantly inhibited CKAP2 overexpression-induced cell proliferation, migration and invasion in SiHa cells. In conclusion, our study suggests that CKAP2 acts as a functional oncogene in cervical carcinoma development and may exert its function by targeting FAK-ERK2 signaling pathway.", "claims": [{"id": "claim-method", "statement": "To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28522860", "locator": "sections[13] \"Bioinformatics analysis\" paragraph 2", "quote": "To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28522860", "locator": "sections[13] \"Bioinformatics analysis\" paragraph 2", "quote": "RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used gene set enrichment analysis (GSEA) on CKAP2 expression in the TCGA and GSE27678 cervical carcinoma datasets; the GSEA identified metastasis-up, cell-cycle, and FAK pathways as associated with elevated CKAP2 expression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28522860", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In the present study, we screened CKAP2 as a new candidate gene which promotes development of cervical carcinoma, in two independent datasets (TCGA and GSE27678)."}, {"asset": "source:pmid:28522860", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Gene set enrichment analysis (GSEA) showed that metastasis, cell cycle and FAK pathways were related with elevated CKAP2 expression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used gene set enrichment analysis (GSEA) on CKAP2 expression in the TCGA and GSE27678 cervical carcinoma datasets; the GSEA identified metastasis-up, cell-cycle, and FAK pathways as associated with elevated CKAP2 expression.", "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:28522860"], "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:GSE27678"], "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:GSE27678"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28522860", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-017-01832-y", "sha256": "sha256:dbb720b11a3f66cb582cd7319467bce4d2d2c09a9cc38afbbb7f82c73fcea26d", "bytes": 43190, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-017-01832-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5437009", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE27678", "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=GSE27678", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE27678", "version": null, "note": "RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM685524", "GSM685525", "GSM685526", "GSM685527", "GSM685528", "GSM685529", "GSM685530", "GSM685531", "GSM685532", "GSM685533", "GSM685534", "GSM685535", "GSM685536", "GSM685537", "GSM685538", "GSM685539", "GSM685540", "GSM685541", "GSM685542", "GSM685543", "GSM685544", "GSM685545", "GSM685546", "GSM685547", "GSM685548", "GSM685549", "GSM685550", "GSM685551", "GSM685552", "GSM685553", "GSM685554", "GSM685555", "GSM685556", "GSM685557", "GSM685558", "GSM685559", "GSM685560", "GSM685561", "GSM685562", "GSM685563", "GSM685564", "GSM685565", "GSM685566", "GSM685567", "GSM685568", "GSM685569", "GSM685570", "GSM685571", "GSM685572", "GSM685573", "GSM685574", "GSM685575", "GSM685576", "GSM685577", "GSM685578", "GSM685579", "GSM685580", "GSM685581", "GSM685582", "GSM685583", "GSM685584", "GSM685585", "GSM685586", "GSM685587", "GSM685588", "GSM685589", "GSM685590", "GSM685591", "GSM685592", "GSM685593", "GSM685594", "GSM685595", "GSM685596", "GSM685597", "GSM685598", "GSM685599", "GSM685600"], "sample_count": 77, "group_sizes": null, "group_sizes_basis": null, "platform": "570;571", "taxon": "Homo sapiens", "title": "Gene expression analysis in a variety of normal, premalignant and squamous cell carcinomas of the cervix", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:28522860:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0fb2a87e96926f57e61309835aee3fbafac89e3eba0e314adbfcf61204b92882", "bytes": 899, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Relationship between CKAP2 and clinical characteristics of cervical carcinoma patients.", "structure": {"pmcid": "PMC5437009", "section_index": 3, "section_title": "Tissue samples", "row_count": 20, "column_count": 5}, "table": {"label": "Table 1", "caption": "Relationship between CKAP2 and clinical characteristics of cervical carcinoma patients.", "rows": [["Factor", "Characteristic", "CKAP2 expression (N)", "P-values"], ["Lower", "Higher"], ["Age (years)", "<35", "60", "42", "0.023"], [">=35", "62", "83"], ["Histology", "Squamous", "105", "110", "0.653"], ["Adenocarcinoma", "17", "15"], ["HPV", "HPV16", "78", "80", "0.536"], ["HPV18", "27", "31"], ["Others", "17", "14"], ["FIGO stage", "Ib~IIa", "21", "6", "0.005"], ["IIb~IIIa", "101", "119"], ["Histological differentiation", "Well", "5", "8", "0.521"], ["Moderate", "78", "73"], ["poor", "39", "44"], ["Lymph node metastasis", "Negative", "115", "78", "<0.0001"], ["Positive", "7", "47"], ["Recurrence", "Yes", "27", "59", "0.002"], ["No", "95", "66"], ["Tumor maximum diameter (cm)", "<4", "98", "80", "0.006"], [">=4", "24", "45"]], "row_count": 20, "column_count": 5, "numeric_cells": 50, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28522860:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:40751c615758ae20705bb3eb5b440f8430c6556271d5aa1c3ecf2c1bb61d7fd7", "bytes": 938, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab2", "version": null, "note": "Primes sequences used in this study.", "structure": {"pmcid": "PMC5437009", "section_index": 8, "section_title": "Reverse transcription-quantitative polymerase chain reaction", "row_count": 15, "column_count": 2}, "table": {"label": "Table 2", "caption": "Primes sequences used in this study.", "rows": [["Gene", "Sequences"], ["CKAP2-forward", "5′-GCCCAAAGAAACCTCGGAAG-3′"], ["CKAP2-reverse", "5′-GCAGGCTCATGCTGAGTAAC-3′"], ["PCNA-forward", "5′-GGTGTTGGAGGCACTCAAGG-3′"], ["PCNA-reverse", "5′-CAGGGTGAGCTGCACCAAAG-3′"], ["MMP-2-forward", "5′-TTGACGGTAAGGACGGACTC-3′"], ["MMP-2-reverse", "5′-GGCGTTCCCATACTTCACAC-3′"], ["MMP-9-forward", "5′-AAGGGCGTCGTGGTTCCAACTC-3′"], ["MMP-9-reverse", "5′-AGCATTGCCGTCCTGGGTGTAG-3′"], ["Snail -forward", "5′-TTCCTGAGCTGGCCTGTCTG-3′"], ["Snail-reverse", "5′-TGGCCTGAGGGTTCCTTGTG-3′"], ["E-cadherin-forward", "5′-GAGAACGCATTGCCACATACAC-3′"], ["E-cadherin-reverse", "5′-AAGAGCACCTTCCATGACAGAC-3′"], ["GAPDH-forward", "5′-CACCCACTCCTCCACCTTTG-3′"], ["GAPDH-reverse", "5′-CCACCACCCTGTTGCTGTAG-3′"]], "row_count": 15, "column_count": 2, "numeric_cells": 18, "header_rows": 1, "locator": "section[8]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:28522860:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f6e289ecffd6bf0c460205bab6b32cfe70877e03f5ea71e6b55571f9eee3c49d", "bytes": 1177, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab3", "version": null, "note": "Univariate and multivariate analysis of clinicopathological factors for overall survival.", "structure": {"pmcid": "PMC5437009", "section_index": 16, "section_title": "CKAP2 expression is upregulated in human cervical carcinoma tissues", "row_count": 11, "column_count": 8}, "table": {"label": "Table 3", "caption": "Univariate and multivariate analysis of clinicopathological factors for overall survival.", "rows": [["Clinicopathological", "Subset", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "p value", "HR", "95% CI", "p value"], ["Age (years)", "<35 vs. >=35", "1.116", "0.628–2.121", "0.589", "", "", ""], ["Histology", "Squamous vs. Adenocarcinoma", "1.128", "0.477–2.691", "0.748", "", "", ""], ["HPV", "HPV16, HPV18 vs. Others", "1.498", "0.774–2.987", "0.231", "", "", ""], ["FIGO stage", "Ib~IIa vs. IIb~IIIa", "3.618", "1.935–6.984", "<0.0001", "2.318", "1.157–4.646", "0.018"], ["Histological differentiation", "Well vs. moderate, poor", "0.725", "0.400–1.382", "0.472", "", "", ""], ["Lymph node metastasis", "Positive vs. negative", "4.253", "2.424–8.308", "<0.0001", "2.236", "1.144–4.926", "0.005"], ["Recurrence", "Yes vs. No", "1.708", "0.802–3.813", "0.139", "", "", ""], ["Tumor maximum diameter (cm)", "<4 vs. >=4", "1.374", "0.624–2.491", "0.539", "", "", ""], ["CKAP2 expression", "High vs. Low", "4.686", "2.175–9.882", "<0.0001", "2.383", "1.234–6.481", "0.013"]], "row_count": 11, "column_count": 8, "numeric_cells": 41, "header_rows": 2, "locator": "section[16]/table-wrap[1]#Tab3"}}], "gaps": ["asset:data:geo:GSE27678 not downloaded", "asset:data:geo:GSE27678 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "formed to calculate the hazard ratio (HR) and the 95% confid", "confidence_interval": "ratio (HR) and the 95% confidence interval (CI) to evaluate the as"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-3", "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"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}, {"id": "method-5", "family": null, "specific": null, "label": "Gene set enrichment analysis (GSEA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To validate the correlation of CKAP2 and signaling pathway involved in pathogenesis in cervical carcinoma, a gene set enrichment analysis (GSEA) was performed to analyze the cervical carcinoma tumors in TCGA dataset."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE27678"], "resolved_accessions": ["GSE27678"], "statements": ["RNA-Seq data from cervical carcinoma tissues and adjacent tissues was downloaded from The Cancer Genome Atlas (TCGA) and the NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) are accessible through GEO Series accession number GSE27678 datasets following approval of this project by the consortium."], "basis": "The paper names GSE27678 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:28522860", "data:geo:GSE27678", "asset:table:pmid:28522860:1", "asset:table:pmid:28522860:2", "asset:table:pmid:28522860:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE27678"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:08Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 92641, "completion_tokens": 3650, "cached_tokens": 1824}}, "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:28522860", "type": "paper", "label": "pmid:28522860"}, {"id": "source:pmid:28522860", "type": "manuscript", "label": "PMID 28522860 full text"}, {"id": "data:geo:GSE27678", "type": "dataset", "label": "GEO GSE27678"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28522860", "type": "paper", "label": "pmid:28522860"}, {"id": "source:pmid:28522860", "type": "manuscript", "label": "PMID 28522860 full text"}, {"id": "data:geo:GSE27678", "type": "dataset", "label": "GEO GSE27678"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28522860", "type": "extraction", "used": ["source:pmid:28522860"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE27678", "type": "accession_resolution", "used": ["data:geo:GSE27678"], "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:28522860", "parent_hash": "sha256:57e211cb31059b7670d69242917a99d42928fc41c6fc5092bec2221dccfb525e", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE27678 licence not read", "asset:data:geo:GSE27678 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["were related with elevated CKAP2 expression. Knockdown of CKAP2 expression significantly inhibited", "E-cadherin. In vivo experiment revealed that knockdown of CKAP2 inhibited C-33A cells proliferation", "C-33A cells infected with pLKO.1-EGFP-CKAP2 shRNA compared with controls as well as the expres", "s increased in response to pLKO.1-EGFP-CKAP2 shRNA infection. The similar results were also fou"], "order_basis": "paper_text_order:797", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["roliferation, migration and invasion both in HeLa and C-33A cells. And depletion of CKAP2 down", "were used in this study. All the cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Hy", "cervical carcinoma cell lines (C-33A, CaSki, HeLa, SiHa and C4-1) obtained from the Cell Bank", "9 and Snail) were significantly decreased in HeLa and C-33A cells infected with pLKO.1-EGFP-CK"], "order_basis": "paper_text_order:902", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ylation of ERK2 (p-ERK2), except E-cadherin. In vivo experiment revealed that knockdown of CKAP2"], "order_basis": "paper_text_order:1091", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["o validate the results in GSEA, we performed Real-time PCR and Western blot analysis in cervical carcin", "MMP-9, Snail and E-cadherin was analyzed by Real-time PCR (A,B) and Western blot (C,D). ***P < 0.001."], "order_basis": "paper_text_order:4263", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ults in GSEA, we performed Real-time PCR and Western blot analysis in cervical carcinoma cells. As sho", ". The similar results were also found in our Western blot analysis in both HeLa and C-33A cells (Fig.", "erin was analyzed by Real-time PCR (A,B) and Western blot (C,D). ***P < 0.001. Electronic supplementar"], "order_basis": "paper_text_order:4281", "id": "assay:5"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}