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

pmid:40316684

PDGF-BB promotes oral submucosal fibrosis by driving phenotypic transformation and autophagy in oral mucosal fibroblasts through downregulation of circHIPK3.

Huamin Zhang · Yutong Zhou · Ni Jian · Canhua Jiang · Qi Wang · Jie Wang

Scientific reports · 2025 doi:10.1038/s41598-025-99753-8

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:40316684
kind
science-record
content_hash
sha256:915b09177e9e1652bcdedb00a53d6ff352109587737b5d3ec2d38f670dfda394
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T20:30:28Z
updated_at
2026-11-01T22:56:28Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
PDGF-BB promotes oral submucosal fibrosis by driving phenotypic transformation and autophagy in oral mucosal fibroblasts through downregulation of circHIPK3.
doi
10.1038/s41598-025-99753-8
pmid
40316684
authors array · 6 items
[0]
Huamin Zhang
[1]
Yutong Zhou
[2]
Ni Jian
[3]
Canhua Jiang
[4]
Qi Wang
[5]
Jie Wang
journal
Scientific reports
year
2025
abstract
Circular RNA HIPK3 (circHIPK3), known to regulate cell proliferation, migration, transformation, and autophagy in various fibrotic conditions. However, its role has not been studied in oral submucous fibrosis (OSF). Therefore, we conducted this study to explore whether platelet-derived growth factor-BB (PDGF-BB) induces human oral submucous fibroblasts (hOMF) proliferation, migration, transformation, and autophagy through circHIPK3 regulation. Treatment of hOMFs with PDGF-BB significantly increased circHIPK3 expression, promoting proliferation, migration, and autophagy. While inhibiting circHIPK3 mitigated these effects, confirming its role in PDGF-BB-mediated pathways. These findings reveal that PDGF-BB regulates hOMFs via circHIPK3, contributing to OSF pathogenesis and offering potential therapeutic targets. The molecular characteristics of circHIPK3 in fibroblasts (FBs) were identified by Agarose Gel Electrophoresis, Sanger Sequencing and Actinomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the expression of target molecules. The proliferation and migration capacity of FBs in oral mucosa were detected by the CCK8 and Cell Scratch Assay. Protein molecules interacting with circHIPK3 and downstream signaling pathways were screened by RNA pull down and mass spectrometry. Data are available via ProteomeXchange with identifier PXD062842. Firstly, the ring structure of circHIPK3 is verified. The expression level of circHIPK3 in OSF tissues and hOMFs was significantly decreased, while the expression level of circHIPK3 was significantly increased after inhibition of platelet-derived growth factor receptor beta‌‌ (PDGFR-β) by Imatinib (IMA). Subsequently, it was confirmed that the overexpression of circHIPK3 could effectively inhibit the proliferation, migration, transformation and autophagy of PDGF-BB-induced hOMFs. Finally, the mechanism study showed that circHIPK3 could inhibit the proliferation, migration, transformation and autophagy of hOMFs by regulating Y-box binding protein 1 (YBX1) protein and extracellular regulated protein kinases (ERK), phosphatidylinositol 3-kinase (PI3K) and p38 mitogen-activated protein kinase (p38 MAPK) signaling pathways. PDGF-BB downregulates circHIPK3 expression and induces proliferation, migration, transformation, and autophagy of oral mucosal FBs via the circHIPK3/YBX1 axis and the circHIPK3/ERK, PI3K, p38 MAPK axis.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40316684
locator
sections[11] "Statistical analysis" paragraph 2
quote
The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:40316684
locator
sections[29] "notes" paragraph 1
quote
The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.
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:40316684
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:PXD062842
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:PXD062842
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:40316684
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1038/s41598-025-99753-8
sha256
sha256:bfe1cb146036eeaff2a64dc7e224b44b88727a1504fd5c09cdf70c9eb1baacad
bytes
51137
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1038/s41598-025-99753-8
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
PMC12048673
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:PXD062842
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=PXD062842
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
PXD062842
version
null
note
The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.
access_statement_kind
data_availability_statement
sample_accessions array · 0 items
sample_count
null
group_sizes
null
group_sizes_basis
null
platform
null
taxon
null
title
LC-MS by circHIPK3 probe method in human oral submucosal fibroblasts
resolution_checked_at
2026-11-01T20:16:18Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:PXD062842 not downloaded
[1]
asset:data:geo:PXD062842 licence not read
analysis object · 4 fields
state
complete
methods array · 1 item
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA).
targets array · 0 items
gaps array · 0 items
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 · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
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: anova.
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]
PXD062842
resolved_accessions array · 1 item
[0]
PXD062842
statements array · 1 item
[0]
The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.
basis
The paper names PXD062842 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:40316684
[1]
data:geo:PXD062842
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:PXD062842
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
2026-11-01T19:51:40Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
14147
completion_tokens
1485
cached_tokens
256
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:40316684
type
paper
label
pmid:40316684
[1] object · 3 fields
id
source:pmid:40316684
type
manuscript
label
PMID 40316684 full text
[2] object · 3 fields
id
data:geo:PXD062842
type
dataset
label
GEO PXD062842
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:40316684
type
paper
label
pmid:40316684
[1] object · 3 fields
id
source:pmid:40316684
type
manuscript
label
PMID 40316684 full text
[2] object · 3 fields
id
data:geo:PXD062842
type
dataset
label
GEO PXD062842
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-40316684
type
extraction
used array · 1 item
[0]
source:pmid:40316684
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-PXD062842
type
accession_resolution
used array · 1 item
[0]
data:geo:PXD062842
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:40316684
parent_hash
sha256:7ae629251a285b4c8d9551cbdc0e0a772e78c55580b1ff57e7d68c597eaa7afc
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:PXD062842 licence not read
[1]
asset:data:geo:PXD062842 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 5 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 · 3 items
[0]
inomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the ex
[1]
mycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the ex
[2]
encing and Actinomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detec
order_basis
paper_text_order:1103
id
assay:1
[1] 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
0.93
evidence array · 1 item
[0]
say. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the expression of target
order_basis
paper_text_order:1130
id
assay:2
[2] object · 11 fields
role
data_generation
definition_id
apoptosis_assay
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]
y of FBs in oral mucosa were detected by the CCK8 and Cell Scratch Assay. Protein molecules in
order_basis
paper_text_order:1283
id
assay:3
[3] object · 11 fields
role
data_generation
definition_id
mass_spectrometry
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]
pathways were screened by RNA pull down and mass spectrometry. Data are available via ProteomeXchange with
order_basis
paper_text_order:1427
id
assay:4
[4] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA).
order_basis
consumes_earlier_output
id
assay:5
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40316684", "kind": "science-record", "revision": 4, "content_hash": "sha256:915b09177e9e1652bcdedb00a53d6ff352109587737b5d3ec2d38f670dfda394", "created_at": "2026-11-01T20:30:28Z", "updated_at": "2026-11-01T22:56:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PDGF-BB promotes oral submucosal fibrosis by driving phenotypic transformation and autophagy in oral mucosal fibroblasts through downregulation of circHIPK3.", "doi": "10.1038/s41598-025-99753-8", "pmid": "40316684", "authors": ["Huamin Zhang", "Yutong Zhou", "Ni Jian", "Canhua Jiang", "Qi Wang", "Jie Wang"], "journal": "Scientific reports", "year": 2025, "abstract": "Circular RNA HIPK3 (circHIPK3), known to regulate cell proliferation, migration, transformation, and autophagy in various fibrotic conditions. However, its role has not been studied in oral submucous fibrosis (OSF). Therefore, we conducted this study to explore whether platelet-derived growth factor-BB (PDGF-BB) induces human oral submucous fibroblasts (hOMF) proliferation, migration, transformation, and autophagy through circHIPK3 regulation. Treatment of hOMFs with PDGF-BB significantly increased circHIPK3 expression, promoting proliferation, migration, and autophagy. While inhibiting circHIPK3 mitigated these effects, confirming its role in PDGF-BB-mediated pathways. These findings reveal that PDGF-BB regulates hOMFs via circHIPK3, contributing to OSF pathogenesis and offering potential therapeutic targets. The molecular characteristics of circHIPK3 in fibroblasts (FBs) were identified by Agarose Gel Electrophoresis, Sanger Sequencing and Actinomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the expression of target molecules. The proliferation and migration capacity of FBs in oral mucosa were detected by the CCK8 and Cell Scratch Assay. Protein molecules interacting with circHIPK3 and downstream signaling pathways were screened by RNA pull down and mass spectrometry. Data are available via ProteomeXchange with identifier PXD062842. Firstly, the ring structure of circHIPK3 is verified. The expression level of circHIPK3 in OSF tissues and hOMFs was significantly decreased, while the expression level of circHIPK3 was significantly increased after inhibition of platelet-derived growth factor receptor beta‌‌ (PDGFR-β) by Imatinib (IMA). Subsequently, it was confirmed that the overexpression of circHIPK3 could effectively inhibit the proliferation, migration, transformation and autophagy of PDGF-BB-induced hOMFs. Finally, the mechanism study showed that circHIPK3 could inhibit the proliferation, migration, transformation and autophagy of hOMFs by regulating Y-box binding protein 1 (YBX1) protein and extracellular regulated protein kinases (ERK), phosphatidylinositol 3-kinase (PI3K) and p38 mitogen-activated protein kinase (p38 MAPK) signaling pathways. PDGF-BB downregulates circHIPK3 expression and induces proliferation, migration, transformation, and autophagy of oral mucosal FBs via the circHIPK3/YBX1 axis and the circHIPK3/ERK, PI3K, p38 MAPK axis.", "claims": [{"id": "claim-method", "statement": "The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40316684", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40316684", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request."}], "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:40316684"], "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:PXD062842"], "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:PXD062842"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40316684", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-025-99753-8", "sha256": "sha256:bfe1cb146036eeaff2a64dc7e224b44b88727a1504fd5c09cdf70c9eb1baacad", "bytes": 51137, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-025-99753-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12048673", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD062842", "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=PXD062842", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD062842", "version": null, "note": "The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "LC-MS by circHIPK3 probe method in human oral submucosal fibroblasts", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD062842 not downloaded", "asset:data:geo:PXD062842 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA)."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PXD062842"], "resolved_accessions": ["PXD062842"], "statements": ["The mass spectrometry proteomics data generated in this study have been deposited to the ProteomeXchange Consortium via the PRIDE repository with the dataset identifier [PXD062842]. The data are currently under private access for peer review and will be made publicly available upon publication of this article. During the review process, reviewers can access the dataset using the credentials below: PRIDE Project Accession: PXD062842 Username: reviewer_pxd062842@ebi.ac.uk Password: XUAPg1EyCIG0 Login Link: https://www.ebi.ac.uk/pride/login. Availability of data and materialsAll data generated and analyzed during the current study are available from the corresponding authors on reasonable request."], "basis": "The paper names PXD062842 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:40316684", "data:geo:PXD062842"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD062842"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:51:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 14147, "completion_tokens": 1485, "cached_tokens": 256}}, "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:40316684", "type": "paper", "label": "pmid:40316684"}, {"id": "source:pmid:40316684", "type": "manuscript", "label": "PMID 40316684 full text"}, {"id": "data:geo:PXD062842", "type": "dataset", "label": "GEO PXD062842"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40316684", "type": "paper", "label": "pmid:40316684"}, {"id": "source:pmid:40316684", "type": "manuscript", "label": "PMID 40316684 full text"}, {"id": "data:geo:PXD062842", "type": "dataset", "label": "GEO PXD062842"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40316684", "type": "extraction", "used": ["source:pmid:40316684"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD062842", "type": "accession_resolution", "used": ["data:geo:PXD062842"], "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:40316684", "parent_hash": "sha256:7ae629251a285b4c8d9551cbdc0e0a772e78c55580b1ff57e7d68c597eaa7afc", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD062842 licence not read", "asset:data:geo:PXD062842 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["inomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the ex", "mycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the ex", "encing and Actinomycin D assay. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detec"], "order_basis": "paper_text_order:1103", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["say. Quantitative real-time PCR(RT-qPCR) and Western Blot were used to detect the expression of target"], "order_basis": "paper_text_order:1130", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["y of FBs in oral mucosa were detected by the CCK8 and Cell Scratch Assay. Protein molecules in"], "order_basis": "paper_text_order:1283", "id": "assay:3"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["pathways were screened by RNA pull down and mass spectrometry. Data are available via ProteomeXchange with"], "order_basis": "paper_text_order:1427", "id": "assay:4"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The data with normal distribution between the two groups were presented by paired sample T-test, and the data with normal distribution between multiple groups were presented by analysis of variance (ANOVA)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}