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

pmid:34580601

Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation.

Zijian Xiao · Qing Ye · Xiaomei Duan · Tao Xiang

Disease markers · 2021 doi:10.1155/2021/4129993

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:34580601
kind
science-record
content_hash
sha256:a08740be93a34564bb67bf556aa396ac8774bc35f1bf7775616fe548992f1457
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:41:54Z
updated_at
2026-11-01T22:04:50Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation.
doi
10.1155/2021/4129993
pmid
34580601
authors array · 4 items
[0]
Zijian Xiao
[1]
Qing Ye
[2]
Xiaomei Duan
[3]
Tao Xiang
journal
Disease markers
year
2021
abstract
Hyperinflammation is related to the development of COVID-19. Resveratrol is considered an anti-inflammatory and antiviral agent. Herein, we used a network pharmacological approach and bioinformatic gene analysis to explore the pharmacological mechanism of Resveratrol in COVID-19 therapy. Potential targets of Resveratrol were obtained from public databases. SARS-CoV-2 differentially expressed genes (DEGs) were screened out via bioinformatic analysis Gene Expression Omnibus (GEO) datasets GSE147507, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; then, protein-protein interaction network was constructed. The common targets, GO terms, and KEGG pathways of Resveratrol targets and SARS-CoV-2 DEGs were confirmed. KEGG Mapper queried the location of common targets in the key pathways. A notable overlap of the GO terms and KEGG pathways between Resveratrol targets and SARS-CoV-2 DEGs was revealed. The shared targets between Resveratrol targets and SARS-CoV-2 mainly involved the IL-17 signaling pathway, NF-kappa B signaling pathway, and TNF signaling pathway. Our study uncovered that Resveratrol is a promising therapeutic candidate for COVID-19 and we also revealed the probable key targets and pathways involved. Ultimately, we bring forward new insights and encourage more studies on Resveratol to benefit COVID-19 patients.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:34580601
locator
sections[4] "2.2. SARS-CoV-2-Related Genes" paragraph 2
quote
Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC).
state
complete
[1] object · 6 fields
id
claim-data-access
statement
The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:34580601
locator
sections[18] "Data Availability" paragraph 2
quote
The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
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:34580601
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:GSE147507
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:GSE147507
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:34580601
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1155/2021/4129993
sha256
sha256:e1509fc3530b7778b52b7c6b6b710ad0b2ba9a4ad6ead92e498f178d4162f978
bytes
33872
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1155/2021/4129993
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
PMC8463930
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE147507
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=GSE147507
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE147507
version
null
note
The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).
access_statement_kind
data_availability_statement
sample_accessions array · 110 items
[0]
GSM4432378
[1]
GSM4432379
[2]
GSM4432380
[3]
GSM4432381
[4]
GSM4432382
[5]
GSM4432383
[6]
GSM4432384
[7]
GSM4432385
[8]
GSM4432386
[9]
GSM4432387
[10]
GSM4432388
[11]
GSM4432389
[12]
GSM4432390
[13]
GSM4432391
[14]
GSM4432392
[15]
GSM4432393
[16]
GSM4432394
[17]
GSM4432395
[18]
GSM4432396
[19]
GSM4432397
[20]
GSM4462336
[21]
GSM4462337
[22]
GSM4462338
[23]
GSM4462339
[24]
GSM4462340
[25]
GSM4462341
[26]
GSM4462342
[27]
GSM4462343
[28]
GSM4462344
[29]
GSM4462345
[30]
GSM4462346
[31]
GSM4462347
[32]
GSM4462348
[33]
GSM4462349
[34]
GSM4462350
[35]
GSM4462351
[36]
GSM4462352
[37]
GSM4462353
[38]
GSM4462354
[39]
GSM4462355
[40]
GSM4462356
[41]
GSM4462357
[42]
GSM4462358
[43]
GSM4462359
[44]
GSM4462360
[45]
GSM4462361
[46]
GSM4462362
[47]
GSM4462363
[48]
GSM4462364
[49]
GSM4462365
[50]
GSM4462366
[51]
GSM4462367
[52]
GSM4462368
[53]
GSM4462369
[54]
GSM4462370
[55]
GSM4462371
[56]
GSM4462372
[57]
GSM4462373
[58]
GSM4462374
[59]
GSM4462375
[60]
GSM4462376
[61]
GSM4462377
[62]
GSM4462378
[63]
GSM4462379
[64]
GSM4462380
[65]
GSM4462381
[66]
GSM4462382
[67]
GSM4462383
[68]
GSM4462384
[69]
GSM4462385
[70]
GSM4462386
[71]
GSM4462387
[72]
GSM4462388
[73]
GSM4462389
[74]
GSM4462390
[75]
GSM4462391
[76]
GSM4462392
[77]
GSM4462393
[78]
GSM4462394
[79]
GSM4462395
[80]
GSM4462396
[81]
GSM4462397
[82]
GSM4462398
[83]
GSM4462399
[84]
GSM4462400
[85]
GSM4462401
[86]
GSM4462402
[87]
GSM4462403
[88]
GSM4462404
[89]
GSM4462405
[90]
GSM4462406
[91]
GSM4462407
[92]
GSM4462408
[93]
GSM4462409
[94]
GSM4462410
[95]
GSM4462411
[96]
GSM4462412
[97]
GSM4462413
[98]
GSM4462414
[99]
GSM4462415
[100]
GSM4462416
[101]
GSM4486157
[102]
GSM4486158
[103]
GSM4486159
[104]
GSM4486160
[105]
GSM4486161
[106]
GSM4486162
[107]
GSM4486163
[108]
GSM4486164
[109]
GSM4486165
sample_count
110
group_sizes
null
group_sizes_basis
null
platform
18573;28369
taxon
Mustela putorius furo; Homo sapiens
title
Transcriptional response to SARS-CoV-2 infection
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:34580601:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:4475382f0c4ed416f4ebd50cfefd2a2637ed506730a1d1814e1d04b7b7407f96
bytes
914
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[12]/table-wrap[1]#tab1
version
null
note
Top 10 overlapping GO terms between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.
structure object · 5 fields
pmcid
PMC8463930
section_index
12
section_title
3.4. Gene Ontology and KEGG Enrichment Analysis of Resveratrol-Related Targets and SARS-CoV-2 DEGs
row_count
11
column_count
3
table object · 8 fields
label
Table 1
caption
Top 10 overlapping GO terms between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.
rows array · 11 items
[0] array · 3 items
[0]
Term
[1]
Description
[2]
p value
[1] array · 3 items
[0]
GO:0019221
[1]
Cytokine-mediated signaling pathway
[2]
2.05074E − 21
[2] array · 3 items
[0]
GO:0060326
[1]
Cell chemotaxis
[2]
5.87962E − 12
[3] array · 3 items
[0]
GO:0030595
[1]
Leukocyte chemotaxis
[2]
7.40744E − 12
[4] array · 3 items
[0]
GO:0032496
[1]
Response to lipopolysaccharide
[2]
1.40404E − 11
[5] array · 3 items
[0]
GO:0006935
[1]
Chemotaxis
[2]
1.68576E − 11
[6] array · 3 items
[0]
GO:0097529
[1]
Myeloid leukocyte migration
[2]
1.7267E − 11
[7] array · 3 items
[0]
GO:0071222
[1]
Cellular response to lipopolysaccharide
[2]
1.7267E − 11
[8] array · 3 items
[0]
GO:0042330
[1]
Taxis
[2]
1.85514E − 11
[9] array · 3 items
[0]
GO:0002237
[1]
Response to molecule of bacterial origin
[2]
5.64373E − 11
[10] array · 3 items
[0]
GO:0071219
[1]
Cellular response to molecule of bacterial origin
[2]
5.83252E − 11
locator
section[12]/table-wrap[1]#tab1
[3] object · 16 fields
id
asset:table:pmid:34580601:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:34331255eb204cc1fc182aeb23244f693f757936861422d5765f51f74e7fc335
bytes
800
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[12]/table-wrap[2]#tab2
version
null
note
Top 10 overlapping KEGG pathways between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.
structure object · 5 fields
pmcid
PMC8463930
section_index
12
section_title
3.4. Gene Ontology and KEGG Enrichment Analysis of Resveratrol-Related Targets and SARS-CoV-2 DEGs
row_count
11
column_count
3
table object · 8 fields
label
Table 2
caption
Top 10 overlapping KEGG pathways between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.
rows array · 11 items
[0] array · 3 items
[0]
Term
[1]
Description
[2]
p value
[1] array · 3 items
[0]
hsa04657
[1]
IL-17 signaling pathway
[2]
9.59366E − 15
[2] array · 3 items
[0]
hsa04668
[1]
TNF signaling pathway
[2]
1.69723E − 13
[3] array · 3 items
[0]
hsa04621
[1]
NOD-like receptor signaling pathway
[2]
6.07599E − 10
[4] array · 3 items
[0]
hsa05162
[1]
Measles
[2]
5.30173E − 09
[5] array · 3 items
[0]
hsa05134
[1]
Legionellosis
[2]
5.45103E − 09
[6] array · 3 items
[0]
hsa05164
[1]
Influenza A
[2]
2.00359E − 07
[7] array · 3 items
[0]
hsa05133
[1]
Pertussis
[2]
1.63392E − 06
[8] array · 3 items
[0]
hsa04064
[1]
NF-kappa B signaling pathway
[2]
1.8066E − 06
[9] array · 3 items
[0]
hsa05140
[1]
Leishmaniasis
[2]
9.37339E − 06
[10] array · 3 items
[0]
hsa05146
[1]
Amoebiasis
[2]
1.38036E − 05
locator
section[12]/table-wrap[2]#tab2
[4] object · 16 fields
id
asset:table:pmid:34580601:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:43884d6cd843a927ee1a050aab83e0d7c8e23e28e5c0f5fe9159610e6123b221
bytes
449
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[13]/table-wrap[1]#tab3
version
null
note
The docking scores of Resveratrol and rapamycin with key proteins.
structure object · 5 fields
pmcid
PMC8463930
section_index
13
section_title
3.5. Molecular Docking Analysis
row_count
7
column_count
4
table object · 8 fields
label
Table 3
caption
The docking scores of Resveratrol and rapamycin with key proteins.
rows array · 7 items
[0] array · 4 items
[0]
Target
[1]
PDB ID
[2]
Drug
[3]
Binding energy (kcal/mol)
[1] array · 4 items
[0]
PLAT
[1]
1OLP
[2]
[3]
-6.93
[2] array · 4 items
[0]
MMP13
[1]
2OW9
[2]
[3]
-6.27
[3] array · 4 items
[0]
PRKCB
[1]
3PFQ
[2]
Resveratrol
[3]
-6.17
[4] array · 4 items
[0]
ICAM1
[1]
5E6D
[2]
[3]
-5.88
[5] array · 4 items
[0]
ITGB3
[1]
4YNY
[2]
[3]
-5.2
[6] array · 4 items
[0]
BCL2A1
[1]
5UUP
[2]
[3]
-4.98
locator
section[13]/table-wrap[1]#tab3
gaps array · 2 items
[0]
asset:data:geo:GSE147507 not downloaded
[1]
asset:data:geo:GSE147507 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
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
0.7
band
medium
quote
protein-protein interaction
[1] object · 10 fields
id
method-2
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
0.7
band
medium
quote
pathway enrichment
[2] object · 10 fields
id
method-3
family
null
specific
null
label
Benjamini-Hochberg method
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
Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC).
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 · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
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: ppi_network.
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]
GSE147507
resolved_accessions array · 1 item
[0]
GSE147507
statements array · 1 item
[0]
The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).
basis
The paper names GSE147507 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 · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
assets array · 5 items
[0]
source:pmid:34580601
[1]
data:geo:GSE147507
[2]
asset:table:pmid:34580601:1
[3]
asset:table:pmid:34580601:2
[4]
asset:table:pmid:34580601:3
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:GSE147507
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
2026-10-31T18:35:18Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
27991
completion_tokens
1357
cached_tokens
792
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:34580601
type
paper
label
pmid:34580601
[1] object · 3 fields
id
source:pmid:34580601
type
manuscript
label
PMID 34580601 full text
[2] object · 3 fields
id
data:geo:GSE147507
type
dataset
label
GEO GSE147507
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:34580601
type
paper
label
pmid:34580601
[1] object · 3 fields
id
source:pmid:34580601
type
manuscript
label
PMID 34580601 full text
[2] object · 3 fields
id
data:geo:GSE147507
type
dataset
label
GEO GSE147507
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-34580601
type
extraction
used array · 1 item
[0]
source:pmid:34580601
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE147507
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE147507
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:34580601
parent_hash
sha256:e5d898dc5db26c31aaa451e743a7ce5b383b0e8e4e3c2febe289d23514fee29b
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE147507 licence not read
[1]
asset:data:geo:GSE147507 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 · 1 item
[0] object · 11 fields
role
analysis
definition_id
network_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
protein-protein interaction
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34580601", "kind": "science-record", "revision": 7, "content_hash": "sha256:a08740be93a34564bb67bf556aa396ac8774bc35f1bf7775616fe548992f1457", "created_at": "2026-11-01T15:41:54Z", "updated_at": "2026-11-01T22:04:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation.", "doi": "10.1155/2021/4129993", "pmid": "34580601", "authors": ["Zijian Xiao", "Qing Ye", "Xiaomei Duan", "Tao Xiang"], "journal": "Disease markers", "year": 2021, "abstract": "Hyperinflammation is related to the development of COVID-19. Resveratrol is considered an anti-inflammatory and antiviral agent. Herein, we used a network pharmacological approach and bioinformatic gene analysis to explore the pharmacological mechanism of Resveratrol in COVID-19 therapy. Potential targets of Resveratrol were obtained from public databases. SARS-CoV-2 differentially expressed genes (DEGs) were screened out via bioinformatic analysis Gene Expression Omnibus (GEO) datasets GSE147507, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; then, protein-protein interaction network was constructed. The common targets, GO terms, and KEGG pathways of Resveratrol targets and SARS-CoV-2 DEGs were confirmed. KEGG Mapper queried the location of common targets in the key pathways. A notable overlap of the GO terms and KEGG pathways between Resveratrol targets and SARS-CoV-2 DEGs was revealed. The shared targets between Resveratrol targets and SARS-CoV-2 mainly involved the IL-17 signaling pathway, NF-kappa B signaling pathway, and TNF signaling pathway. Our study uncovered that Resveratrol is a promising therapeutic candidate for COVID-19 and we also revealed the probable key targets and pathways involved. Ultimately, we bring forward new insights and encourage more studies on Resveratol to benefit COVID-19 patients.", "claims": [{"id": "claim-method", "statement": "Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34580601", "locator": "sections[4] \"2.2. SARS-CoV-2-Related Genes\" paragraph 2", "quote": "Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34580601", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34580601"], "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:GSE147507"], "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:GSE147507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34580601", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2021/4129993", "sha256": "sha256:e1509fc3530b7778b52b7c6b6b710ad0b2ba9a4ad6ead92e498f178d4162f978", "bytes": 33872, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2021/4129993", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8463930", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE147507", "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=GSE147507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE147507", "version": null, "note": "The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4432378", "GSM4432379", "GSM4432380", "GSM4432381", "GSM4432382", "GSM4432383", "GSM4432384", "GSM4432385", "GSM4432386", "GSM4432387", "GSM4432388", "GSM4432389", "GSM4432390", "GSM4432391", "GSM4432392", "GSM4432393", "GSM4432394", "GSM4432395", "GSM4432396", "GSM4432397", "GSM4462336", "GSM4462337", "GSM4462338", "GSM4462339", "GSM4462340", "GSM4462341", "GSM4462342", "GSM4462343", "GSM4462344", "GSM4462345", "GSM4462346", "GSM4462347", "GSM4462348", "GSM4462349", "GSM4462350", "GSM4462351", "GSM4462352", "GSM4462353", "GSM4462354", "GSM4462355", "GSM4462356", "GSM4462357", "GSM4462358", "GSM4462359", "GSM4462360", "GSM4462361", "GSM4462362", "GSM4462363", "GSM4462364", "GSM4462365", "GSM4462366", "GSM4462367", "GSM4462368", "GSM4462369", "GSM4462370", "GSM4462371", "GSM4462372", "GSM4462373", "GSM4462374", "GSM4462375", "GSM4462376", "GSM4462377", "GSM4462378", "GSM4462379", "GSM4462380", "GSM4462381", "GSM4462382", "GSM4462383", "GSM4462384", "GSM4462385", "GSM4462386", "GSM4462387", "GSM4462388", "GSM4462389", "GSM4462390", "GSM4462391", "GSM4462392", "GSM4462393", "GSM4462394", "GSM4462395", "GSM4462396", "GSM4462397", "GSM4462398", "GSM4462399", "GSM4462400", "GSM4462401", "GSM4462402", "GSM4462403", "GSM4462404", "GSM4462405", "GSM4462406", "GSM4462407", "GSM4462408", "GSM4462409", "GSM4462410", "GSM4462411", "GSM4462412", "GSM4462413", "GSM4462414", "GSM4462415", "GSM4462416", "GSM4486157", "GSM4486158", "GSM4486159", "GSM4486160", "GSM4486161", "GSM4486162", "GSM4486163", "GSM4486164", "GSM4486165"], "sample_count": 110, "group_sizes": null, "group_sizes_basis": null, "platform": "18573;28369", "taxon": "Mustela putorius furo; Homo sapiens", "title": "Transcriptional response to SARS-CoV-2 infection", "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:34580601:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4475382f0c4ed416f4ebd50cfefd2a2637ed506730a1d1814e1d04b7b7407f96", "bytes": 914, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab1", "version": null, "note": "Top 10 overlapping GO terms between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.", "structure": {"pmcid": "PMC8463930", "section_index": 12, "section_title": "3.4. Gene Ontology and KEGG Enrichment Analysis of Resveratrol-Related Targets and SARS-CoV-2 DEGs", "row_count": 11, "column_count": 3}, "table": {"label": "Table 1", "caption": "Top 10 overlapping GO terms between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.", "rows": [["Term", "Description", "p value"], ["GO:0019221", "Cytokine-mediated signaling pathway", "2.05074E − 21"], ["GO:0060326", "Cell chemotaxis", "5.87962E − 12"], ["GO:0030595", "Leukocyte chemotaxis", "7.40744E − 12"], ["GO:0032496", "Response to lipopolysaccharide", "1.40404E − 11"], ["GO:0006935", "Chemotaxis", "1.68576E − 11"], ["GO:0097529", "Myeloid leukocyte migration", "1.7267E − 11"], ["GO:0071222", "Cellular response to lipopolysaccharide", "1.7267E − 11"], ["GO:0042330", "Taxis", "1.85514E − 11"], ["GO:0002237", "Response to molecule of bacterial origin", "5.64373E − 11"], ["GO:0071219", "Cellular response to molecule of bacterial origin", "5.83252E − 11"]], "row_count": 11, "column_count": 3, "numeric_cells": 20, "header_rows": 1, "locator": "section[12]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:34580601:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34331255eb204cc1fc182aeb23244f693f757936861422d5765f51f74e7fc335", "bytes": 800, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tab2", "version": null, "note": "Top 10 overlapping KEGG pathways between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.", "structure": {"pmcid": "PMC8463930", "section_index": 12, "section_title": "3.4. Gene Ontology and KEGG Enrichment Analysis of Resveratrol-Related Targets and SARS-CoV-2 DEGs", "row_count": 11, "column_count": 3}, "table": {"label": "Table 2", "caption": "Top 10 overlapping KEGG pathways between Resveratrol-related targets and SARS-CoV-2 DEGs ranked by p value.", "rows": [["Term", "Description", "p value"], ["hsa04657", "IL-17 signaling pathway", "9.59366E − 15"], ["hsa04668", "TNF signaling pathway", "1.69723E − 13"], ["hsa04621", "NOD-like receptor signaling pathway", "6.07599E − 10"], ["hsa05162", "Measles", "5.30173E − 09"], ["hsa05134", "Legionellosis", "5.45103E − 09"], ["hsa05164", "Influenza A", "2.00359E − 07"], ["hsa05133", "Pertussis", "1.63392E − 06"], ["hsa04064", "NF-kappa B signaling pathway", "1.8066E − 06"], ["hsa05140", "Leishmaniasis", "9.37339E − 06"], ["hsa05146", "Amoebiasis", "1.38036E − 05"]], "row_count": 11, "column_count": 3, "numeric_cells": 21, "header_rows": 1, "locator": "section[12]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:34580601:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43884d6cd843a927ee1a050aab83e0d7c8e23e28e5c0f5fe9159610e6123b221", "bytes": 449, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab3", "version": null, "note": "The docking scores of Resveratrol and rapamycin with key proteins.", "structure": {"pmcid": "PMC8463930", "section_index": 13, "section_title": "3.5. Molecular Docking Analysis", "row_count": 7, "column_count": 4}, "table": {"label": "Table 3", "caption": "The docking scores of Resveratrol and rapamycin with key proteins.", "rows": [["Target", "PDB ID", "Drug", "Binding energy (kcal/mol)"], ["PLAT", "1OLP", "", "-6.93"], ["MMP13", "2OW9", "", "-6.27"], ["PRKCB", "3PFQ", "Resveratrol", "-6.17"], ["ICAM1", "5E6D", "", "-5.88"], ["ITGB3", "4YNY", "", "-5.2"], ["BCL2A1", "5UUP", "", "-4.98"]], "row_count": 7, "column_count": 4, "numeric_cells": 13, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab3"}}], "gaps": ["asset:data:geo:GSE147507 not downloaded", "asset:data:geo:GSE147507 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}, {"id": "method-3", "family": null, "specific": null, "label": "Benjamini-Hochberg method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Adjusted original p values were obtained via the Benjamini-Hochberg method; the false discovery rate (FDR) procedure was used to calculate fold changes (FC)."}}], "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE147507"], "resolved_accessions": ["GSE147507"], "statements": ["The data used in this study were obtained from open public databases, and data acquisition is explained in the manuscript. SARS-CoV-2 differentially expressed genes (DEGs) were taken from Gene Expression Omnibus (GEO) datasets GSE147507. The molecular structure of Resveratrol was downloaded from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/). TargetNet (http://targetnet.scbdd.com/) was used to predict potential targets for Resveratrol. The molecular structures of the targets were obtained from the Protein Data Bank (http://www.rcsb.org/)."], "basis": "The paper names GSE147507 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34580601", "data:geo:GSE147507", "asset:table:pmid:34580601:1", "asset:table:pmid:34580601:2", "asset:table:pmid:34580601:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE147507"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 27991, "completion_tokens": 1357, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34580601", "type": "paper", "label": "pmid:34580601"}, {"id": "source:pmid:34580601", "type": "manuscript", "label": "PMID 34580601 full text"}, {"id": "data:geo:GSE147507", "type": "dataset", "label": "GEO GSE147507"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34580601", "type": "paper", "label": "pmid:34580601"}, {"id": "source:pmid:34580601", "type": "manuscript", "label": "PMID 34580601 full text"}, {"id": "data:geo:GSE147507", "type": "dataset", "label": "GEO GSE147507"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34580601", "type": "extraction", "used": ["source:pmid:34580601"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE147507", "type": "accession_resolution", "used": ["data:geo:GSE147507"], "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:34580601", "parent_hash": "sha256:e5d898dc5db26c31aaa451e743a7ce5b383b0e8e4e3c2febe289d23514fee29b", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE147507 licence not read", "asset:data:geo:GSE147507 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}