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pmid:32733557

Gene Expression, Network Analysis, and Drug Discovery of Neurofibromatosis Type 2-Associated Vestibular Schwannomas Based on Bioinformatics Analysis.

Qiao Huang · Si-Jia Zhai · Xing-Wei Liao · Yu-Chao Liu · Shi-Hua Yin

Journal of oncology · 2020 doi:10.1155/2020/5976465

Paper

complete

Experiment

partial

Data

partial

Analysis

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.2
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pmid:32733557
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science-record
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7
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2026-11-01T15:41:06Z
updated_at
2026-11-01T22:01:58Z
generator object · 2 fields
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paper object · 10 fields
state
complete
title
Gene Expression, Network Analysis, and Drug Discovery of Neurofibromatosis Type 2-Associated Vestibular Schwannomas Based on Bioinformatics Analysis.
doi
10.1155/2020/5976465
pmid
32733557
authors array · 5 items
[0]
Qiao Huang
[1]
Si-Jia Zhai
[2]
Xing-Wei Liao
[3]
Yu-Chao Liu
[4]
Shi-Hua Yin
journal
Journal of oncology
year
2020
abstract
Neurofibromatosis Type 2- (NF2-) associated vestibular schwannomas (VSs) are histologically benign tumors. This study aimed to determine disease-related genes, pathways, and potential therapeutic drugs associated with NF2-VSs using the bioinformatics method. Microarray data of GSE108524 were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were screened using GEO2R. The functional enrichment and pathway enrichment of DEGs were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG). Furthermore, the STRING and Cytoscape were used to analyze the protein-protein interaction (PPI) network of all differentially expressed genes and identify hub genes. Finally, the enriched gene sets belonging to the identified pathways were queried against the Drug-Gene Interaction database to find drug candidates for topical use in NF2-associated VSs. A total of 542 DEGs were identified, including 13 upregulated and 329 downregulated genes, which were mainly enriched in terms of focal adhesion, PI3K-Akt signaling pathway, ECM-receptor interaction, Toll-like receptor signaling pathway, Rap1 signaling pathway, and regulation of actin cytoskeleton. 28 hub genes were identified based on the subset of PPI network, and 31 drugs were selected based on the Drug-Gene Interaction database. Drug discovery using bioinformatics methods facilitates the identification of existing or potential therapeutic drugs to improve NF2 treatment.
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claim-data-access
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The data used to support the findings of this study are available from the corresponding author upon request.
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methodological
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evidence array · 1 item
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asset
source:pmid:32733557
locator
sections[19] "Data Availability" paragraph 2
quote
The data used to support the findings of this study are available from the corresponding author upon request.
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null
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read_published_estimate
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Read the published estimate from the source
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null
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The claim, method and evidence span published with the source article.
duration_hours
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parameters object · 0 fields
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source:pmid:32733557
outputs array · 1 item
[0]
the published estimate and its evidence
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[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
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complete
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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 object · 0 fields
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[0]
data:geo:GSE108524
outputs array · 1 item
[0]
the source data with its repository provenance
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run_analysis
order
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name
Run the published analysis
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Apply the paper's statistical method to the resolved series and compare the result with the published target.
duration_hours
null
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE108524
outputs array · 1 item
[0]
the replicated result and its comparison
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conditions object · 0 fields
gaps array · 1 item
[0]
step:run_analysis blocked on method:student_t
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partial
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source:pmid:32733557
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https://doi.org/10.1155/2020/5976465
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10.1155/2020/5976465
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Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC7378604
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
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data:geo:GSE108524
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raw
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geo-series
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application/vnd.ncbi.geo-series+json
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https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108524
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reader_required
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version
null
note
The data used to support the findings of this study are available from the corresponding author upon request.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
The data used to support the findings of this study are available from the corresponding author upon request.
access_statement_kind
data_availability_statement
sample_accessions array · 31 items
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GSM2893469
[1]
GSM2893470
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GSM2893475
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GSM2893476
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GSM2893477
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GSM2893479
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GSM2893480
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GSM2893481
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GSM2902751
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GSM2902754
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GSM2902760
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GSM2902762
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GSM2902763
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GSM2902764
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GSM2902765
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GSM2902766
sample_count
31
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null
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null
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17586
taxon
Homo sapiens
title
Targeting the cMET pathway augments radiation response without adverse effect on hearing in NF2 schwannoma models
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
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licence_read
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GO analysis of differentially expressed genes.
structure object · 5 fields
pmcid
PMC7378604
section_index
13
section_title
3.2. Functional Annotation and Pathway Enrichment Analysis of DEGs
row_count
25
column_count
5
table object · 8 fields
label
Table 1
caption
GO analysis of differentially expressed genes.
rows array · 25 items
[0] array · 5 items
[0]
Category
[1]
Term
[2]
Count
[3]
P value
[4]
FDR
[1] array · 5 items
[0]
BP
[1]
GO:0007155 ∼ cell adhesion
[2]
38
[3]
<0.001
[4]
<0.001
[2] array · 5 items
[0]
BP
[1]
GO:0006954 ∼ inflammatory response
[2]
34
[3]
<0.001
[4]
<0.001
[3] array · 5 items
[0]
BP
[1]
GO:0006955 ∼ immune response
[2]
32
[3]
<0.001
[4]
<0.001
[4] array · 5 items
[0]
BP
[1]
GO:0007165 ∼ signal transduction
[2]
58
[3]
<0.001
[4]
0.0054
[5] array · 5 items
[0]
BP
[1]
GO:0051897 ∼ positive regulation of protein kinase B signaling
[2]
12
[3]
<0.001
[4]
0.0203
[6] array · 5 items
[0]
BP
[1]
GO:0070374 ∼ positive regulation of ERK1 and ERK2 cascade
[2]
17
[3]
<0.001
[4]
0.0261
[7] array · 5 items
[0]
BP
[1]
GO:0043547 ∼ positive regulation of GTPase activity
[2]
34
[3]
<0.001
[4]
0.0265
[8] array · 5 items
[0]
BP
[1]
GO:0030198 ∼ extracellular matrix organization
[2]
18
[3]
<0.001
[4]
0.0285
[9] array · 5 items
[0]
BP
[1]
GO:0030335 ∼ positive regulation of cell migration
[2]
17
[3]
<0.001
[4]
0.0488
[10] array · 5 items
[0]
CC
[1]
GO:0005615 ∼ extracellular space
[2]
87
[3]
<0.001
[4]
<0.001
[11] array · 5 items
[0]
CC
[1]
GO:0005887 ∼ integral component of plasma membrane
[2]
88
[3]
<0.001
[4]
<0.001
[12] array · 5 items
[0]
CC
[1]
GO:0005886 ∼ plasma membrane
[2]
177
[3]
<0.001
[4]
<0.001
[13] array · 5 items
[0]
CC
[1]
GO:0005578 ∼ proteinaceous extracellular matrix
[2]
31
[3]
<0.001
[4]
<0.001
[14] array · 5 items
[0]
CC
[1]
GO:0009986 ∼ cell surface
[2]
42
[3]
<0.001
[4]
<0.001
[15] array · 5 items
[0]
CC
[1]
GO:0070062 ∼ extracellular exosome
[2]
121
[3]
<0.001
[4]
<0.001
[16] array · 5 items
[0]
CC
[1]
GO:0005576 ∼ extracellular region
[2]
81
[3]
<0.001
[4]
<0.001
[17] array · 5 items
[0]
CC
[1]
GO:0031012 ∼ extracellular matrix
[2]
28
[3]
<0.001
[4]
<0.001
[18] array · 5 items
[0]
CC
[1]
GO:0009897 ∼ external side of plasma membrane
[2]
21
[3]
<0.001
[4]
<0.001
[19] array · 5 items
[0]
CC
[1]
GO:0045121 ∼ membrane raft
[2]
20
[3]
<0.001
[4]
0.0020
[20] array · 5 items
[0]
CC
[1]
GO:0016021 ∼ integral component of membrane
[2]
179
[3]
<0.001
[4]
0.0020
[21] array · 5 items
[0]
CC
[1]
GO:0005925 ∼ focal adhesion
[2]
27
[3]
<0.001
[4]
0.0122
[22] array · 5 items
[0]
CC
[1]
GO:0045202 ∼ synapse
[2]
17
[3]
<0.001
[4]
0.0224
[23] array · 5 items
[0]
MF
[1]
GO:0008201 ∼ heparin binding
[2]
20
[3]
<0.001
[4]
<0.001
[24] array · 5 items
[0]
MF
[1]
GO:0005178 ∼ integrin binding
[2]
14
[3]
<0.001
[4]
0.0041
row_count
25
column_count
5
numeric_cells
96
header_rows
1
locator
section[13]/table-wrap[1]#tab1
[3] object · 16 fields
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asset:table:pmid:32733557:2
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null
sha256
sha256:38eab4d5acc4ade302993efe0a3aca5e7d36155221c9cbebf252ae8111114964
bytes
3996
access
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read_table
reader_status
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identifier
section[13]/table-wrap[2]#tab2
version
null
note
KEGG pathway analysis of differentially expressed genes.
structure object · 5 fields
pmcid
PMC7378604
section_index
13
section_title
3.2. Functional Annotation and Pathway Enrichment Analysis of DEGs
row_count
29
column_count
4
table object · 8 fields
label
Table 2
caption
KEGG pathway analysis of differentially expressed genes.
rows array · 29 items
[0] array · 4 items
[0]
Term
[1]
Count
[2]
P value
[3]
Genes
[1] array · 4 items
[0]
hsa05150: staphylococcus aureus infection
[1]
13
[2]
<0.001
[3]
C3AR1, C3, HLA-DRB3, FPR1, C1R, C1S, HLA-DQA1, FCGR1A, CFH, FCGR3A, CFD, SELPLG, FCGR3B
[2] array · 4 items
[0]
hsa04145: phagosome
[1]
19
[2]
<0.001
[3]
MRC1, NOS1, OLR1, C3, TUBB2A, HLA-DRB3, TLR2, HLA-C, C1R, TLR6, HLA-DQA1, CYBB, CD36, FCGR1A, COMP, CLEC7A, FCGR3A, FCGR3B, THBS4
[3] array · 4 items
[0]
hsa04514: cell adhesion molecules (CAMs)
[1]
16
[2]
<0.001
[3]
CLDN19, HLA-DRB3, HLA-C, L1CAM, NLGN3, CDH2, HLA-DQA1, CDH5, ALCAM, NCAM1, CD86, CD34, ITGA8, CLDN1, CD4, SELPLG
[4] array · 4 items
[0]
hsa04640: hematopoietic cell lineage
[1]
12
[2]
<0.001
[3]
CR1, CD37, CD36, CD34, HLA-DRB3, FCGR1A, MME, IL1B, CD4, ANPEP, CSF2RA, CSF1R
[5] array · 4 items
[0]
hsa05144: malaria
[1]
9
[2]
<0.001
[3]
CR1, CD36, COMP, TLR2, IL1B, HBA2, HBA1, HBB, THBS4
[6] array · 4 items
[0]
hsa04610: complement and coagulation cascades
[1]
10
[2]
<0.001
[3]
C3AR1, VWF, CR1, C3, F13A1, CFH, TFPI, C1R, C1S, CFD
[7] array · 4 items
[0]
hsa04510: focal adhesion
[1]
17
[2]
0.0017
[3]
PIK3CG, EGFR, CAV1, TNXB, TNC, FLNB, MYL9, VWF, CCND1, PAK3, CCND2, COMP, ITGA8, COL6A3, PDGFRA, SPP1, THBS4
[8] array · 4 items
[0]
hsa04060: cytokine-cytokine receptor interaction
[1]
18
[2]
0.0022
[3]
EGFR, CCL3, TGFBR1, LIFR, EDA2R, CCL4L1, CCL4, CXCL12, IL17RA, LEP, PPBP, CXCL14, CCL3L3, CX3CR1, PDGFRA, IL1B, CSF2RA, CSF1R
[9] array · 4 items
[0]
hsa05140: leishmaniasis
[1]
9
[2]
0.0027
[3]
CR1, C3, HLA-DRB3, FCGR1A, TLR2, IL1B, FCGR3A, FCGR3B, HLA-DQA1
[10] array · 4 items
[0]
hsa04151: PI3K-akt signaling pathway
[1]
23
[2]
0.0033
[3]
EGFR, PIK3CG, FGF7, TNXB, TNC, TLR2, FGF10, IRS1, DDIT4, VWF, CCND1, LPAR5, CCND2, COMP, ITGA8, COL6A3, PDGFRA, MDM2, ANGPT1, FGF1, SPP1, THBS4, CSF1R
[11] array · 4 items
[0]
hsa00350: tyrosine metabolism
[1]
6
[2]
0.0063
[3]
MAOA, AOX1, ADH1C, ADH1B, ADH1A, AOC3
[12] array · 4 items
[0]
hsa03320: PPAR signaling pathway
[1]
8
[2]
0.0075
[3]
LPL, CD36, OLR1, PLIN1, SLC27A6, FABP4, ACADL, ADIPOQ
[13] array · 4 items
[0]
hsa04512: ECM-receptor interaction
[1]
9
[2]
0.0094
[3]
VWF, CD36, TNXB, COMP, TNC, ITGA8, COL6A3, SPP1, THBS4
[14] array · 4 items
[0]
hsa04620: Toll-like receptor signaling pathway
[1]
10
[2]
0.0100
[3]
PIK3CG, CD86, CCL3, CCL3L3, TLR2, CCL4L1, IL1B, TLR6, CCL4, SPP1
[15] array · 4 items
[0]
hsa05323: rheumatoid arthritis
[1]
9
[2]
0.0101
[3]
CD86, CCL3, HLA-DRB3, CCL3L3, TLR2, IL1B, ANGPT1, CXCL12, HLA-DQA1
[16] array · 4 items
[0]
hsa05218: melanoma
[1]
8
[2]
0.0103
[3]
PIK3CG, EGFR, CCND1, FGF7, PDGFRA, MDM2, FGF10, FGF1
[17] array · 4 items
[0]
hsa04015: Rap1 signaling pathway
[1]
15
[2]
0.0126
[3]
FYB, PIK3CG, EGFR, FGF7, FPR1, FGF10, APBB1IP, DOCK4, PLCB4, LPAR5, RASGRP3, PDGFRA, ANGPT1, FGF1, CSF1R
[18] array · 4 items
[0]
hsa05416: viral myocarditis
[1]
7
[2]
0.0126
[3]
CAV1, CD86, CCND1, HLA-DRB3, SGCD, HLA-C, HLA-DQA1
[19] array · 4 items
[0]
hsa04730: long-term depression
[1]
7
[2]
0.0160
[3]
PLA2G4A, PLCB4, NOS1, GRIA2, LYN, GUCY1A2, GUCY1B3
[20] array · 4 items
[0]
hsa05206: microRNAs in cancer
[1]
18
[2]
0.0176
[3]
EGFR, TNXB, CYP1B1, TNC, MIRLET7F1, MIR99A, ZEB1, MIR222, MIR221, IRS1, DDIT4, NOTCH3, CCND1, CCND2, PDGFRA, MDM2, MARCKS, MIR181B2
[21] array · 4 items
[0]
hsa05152: tuberculosis
[1]
13
[2]
0.0178
[3]
MRC1, CR1, ITGAX, C3, FCGR1A, HLA-DRB3, TLR2, IL1B, CLEC7A, FCGR3A, TLR6, FCGR3B, HLA-DQA1
[22] array · 4 items
[0]
hsa05205: proteoglycans in cancer
[1]
14
[2]
0.0191
[3]
PIK3CG, EGFR, CAV1, LUM, FZD1, TLR2, DCN, FLNB, CCND1, CBLB, GPC3, RRAS2, MDM2, PTCH1
[23] array · 4 items
[0]
hsa05143: African trypanosomiasis
[1]
5
[2]
0.0250
[3]
PLCB4, IL1B, HBA2, HBA1, HBB
[24] array · 4 items
[0]
hsa05332: graft-versus-host disease
[1]
5
[2]
0.0250
[3]
CD86, HLA-DRB3, IL1B, HLA-C, HLA-DQA1
[25] array · 4 items
[0]
hsa05142: Chagas disease (American trypanosomiasis)
[1]
9
[2]
0.0254
[3]
PIK3CG, CCL3, PLCB4, C3, TGFBR1, CCL3L3, TLR2, IL1B, TLR6
[26] array · 4 items
[0]
hsa05200: pathways in cancer
[1]
22
[2]
0.0267
[3]
EGFR, PIK3CG, FGF7, TGFBR1, FZD1, RUNX1T1, FGF10, CXCL12, CBLB, CCND1, PLCB4, LPAR5, RASGRP3, SLC2A1, PDGFRA, MDM2, PTCH1, PTCH2, HHIP, FGF1, CSF2RA, CSF1R
[27] array · 4 items
[0]
hsa04810: regulation of actin cytoskeleton
[1]
14
[2]
0.0282
[3]
PIK3CG, EGFR, FGF7, FGF10, NCKAP1L, MYL9, ARPC1B, ITGAX, CHRM3, PAK3, ITGA8, RRAS2, PDGFRA, FGF1
[28] array · 4 items
[0]
hsa04380: osteoclast differentiation
[1]
10
[2]
0.0349
[3]
PIK3CG, CYBB, FCGR1A, TGFBR1, IL1B, FCGR3A, TREM2, FCGR3B, CSF1R, BLNK
row_count
29
column_count
4
numeric_cells
102
header_rows
1
locator
section[13]/table-wrap[2]#tab2
[4] object · 16 fields
id
asset:table:pmid:32733557:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:9d3a21b08782ea5be2219e4ee6b46ec0689075062d46d05a067815ddb5e4b738
bytes
952
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[14]/table-wrap[1]#tab3
version
null
note
28 hub genes with connectivity degree ≥20.
structure object · 5 fields
pmcid
PMC7378604
section_index
14
section_title
3.3. PPI Network Analysis
row_count
29
column_count
4
table object · 8 fields
label
Table 3
caption
28 hub genes with connectivity degree ≥20.
rows array · 29 items
[0] array · 4 items
[0]
Number
[1]
Gene
[2]
Degree of connectivity
[3]
Regulation
[1] array · 4 items
[0]
1
[1]
EGFR
[2]
59
[3]
Down
[2] array · 4 items
[0]
2
[1]
IL1B
[2]
53
[3]
Up
[3] array · 4 items
[0]
3
[1]
PIK3CG
[2]
49
[3]
Up
[4] array · 4 items
[0]
4
[1]
CSF1R
[2]
40
[3]
Up
[5] array · 4 items
[0]
5
[1]
CXCL12
[2]
39
[3]
Down
[6] array · 4 items
[0]
6
[1]
CD34
[2]
36
[3]
Down
[7] array · 4 items
[0]
7
[1]
EDN1
[2]
36
[3]
Down
[8] array · 4 items
[0]
8
[1]
ITGAX
[2]
34
[3]
Up
[9] array · 4 items
[0]
9
[1]
ACACB
[2]
34
[3]
Down
[10] array · 4 items
[0]
10
[1]
LYN
[2]
32
[3]
Up
[11] array · 4 items
[0]
11
[1]
FCGR3A
[2]
32
[3]
Up
[12] array · 4 items
[0]
12
[1]
DCN
[2]
30
[3]
Down
[13] array · 4 items
[0]
13
[1]
CD36
[2]
30
[3]
Down
[14] array · 4 items
[0]
14
[1]
VWF
[2]
30
[3]
Down
[15] array · 4 items
[0]
15
[1]
CD86
[2]
29
[3]
Up
[16] array · 4 items
[0]
16
[1]
TLR2
[2]
29
[3]
Up
[17] array · 4 items
[0]
17
[1]
ACTA2
[2]
29
[3]
Down
[18] array · 4 items
[0]
18
[1]
LEP
[2]
29
[3]
Down
[19] array · 4 items
[0]
19
[1]
FCGR3B
[2]
26
[3]
Up
[20] array · 4 items
[0]
20
[1]
NCAM1
[2]
25
[3]
Up
[21] array · 4 items
[0]
21
[1]
CAV1
[2]
24
[3]
Down
[22] array · 4 items
[0]
22
[1]
HBA1
[2]
23
[3]
Up
[23] array · 4 items
[0]
23
[1]
ACTG2
[2]
22
[3]
Down
[24] array · 4 items
[0]
24
[1]
SPP1
[2]
21
[3]
Up
[25] array · 4 items
[0]
25
[1]
C3
[2]
21
[3]
Up
[26] array · 4 items
[0]
26
[1]
PDGFRA
[2]
20
[3]
Down
[27] array · 4 items
[0]
27
[1]
CCND1
[2]
20
[3]
Up
[28] array · 4 items
[0]
28
[1]
RRAS2
[2]
20
[3]
Up
row_count
29
column_count
4
numeric_cells
60
header_rows
1
locator
section[14]/table-wrap[1]#tab3
gaps array · 2 items
[0]
asset:data:geo:GSE108524 not downloaded
[1]
asset:data:geo:GSE108524 licence not read
analysis object · 4 fields
state
partial
methods array · 3 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
student_t_test
label
Group comparison
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
expressible
false
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
0.8
band
high
quote
Student's t-test
[1] object · 10 fields
id
method-2
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
expressible
true
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
[2] object · 10 fields
id
method-3
family
network_analysis
specific
pathway_enrichment
label
Network / pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
expressible
true
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
pathway enrichment
targets array · 0 items
gaps array · 1 item
[0]
method.student_t
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
availability_state
owned
tier_unlocked
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocking_axis
none
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
false
required_operations array · 0 items
missing_operations array · 1 item
[0]
student_t
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test.
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]
GSE108524
resolved_accessions array · 1 item
[0]
GSE108524
statements array · 1 item
[0]
The data used to support the findings of this study are available from the corresponding author upon request.
basis
The paper names GSE108524 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 · 0 items
assets array · 5 items
[0]
source:pmid:32733557
[1]
data:geo:GSE108524
[2]
asset:table:pmid:32733557:1
[3]
asset:table:pmid:32733557:2
[4]
asset:table:pmid:32733557:3
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
operation
student_t
unlocks_papers
null
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE108524
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
2026-10-31T19:07:17Z
independence
single_reader
evidence_check object · 2 fields
method
null
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
18267
completion_tokens
1271
cached_tokens
792
human_critique
null
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:32733557
type
paper
label
pmid:32733557
[1] object · 3 fields
id
source:pmid:32733557
type
manuscript
label
PMID 32733557 full text
[2] object · 3 fields
id
data:geo:GSE108524
type
dataset
label
GEO GSE108524
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:32733557
type
paper
label
pmid:32733557
[1] object · 3 fields
id
source:pmid:32733557
type
manuscript
label
PMID 32733557 full text
[2] object · 3 fields
id
data:geo:GSE108524
type
dataset
label
GEO GSE108524
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-32733557
type
extraction
used array · 1 item
[0]
source:pmid:32733557
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE108524
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE108524
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:32733557
parent_hash
sha256:c2cd6cdf00f45c361fe72c73599e7d61afb056e0068eb856f14e11841b6f3bb2
fork_of
null
generation
6
gaps array · 8 items
[0]
asset:data:geo:GSE108524 licence not read
[1]
asset:data:geo:GSE108524 not downloaded
[2]
execution.not_run
[3]
method.student_t
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
[7]
step:run_analysis blocked on method:student_t
assays array · 2 items
[0] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
definition_digest
null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
ith NF2-VSs using the bioinformatics method. Microarray data of GSE108524 were downloaded from the G
order_basis
paper_text_order:364
id
assay:1
[1] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
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null
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
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0.8
evidence array · 1 item
[0]
Student's t-test
order_basis
consumes_earlier_output
id
assay:2
Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32733557", "kind": "science-record", "revision": 7, "content_hash": "sha256:ca3ca0d562cb4379d8f5082b17b80bf27e6edf48b89095bc1df73bfbd73aa256", "created_at": "2026-11-01T15:41:06Z", "updated_at": "2026-11-01T22:01:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene Expression, Network Analysis, and Drug Discovery of Neurofibromatosis Type 2-Associated Vestibular Schwannomas Based on Bioinformatics Analysis.", "doi": "10.1155/2020/5976465", "pmid": "32733557", "authors": ["Qiao Huang", "Si-Jia Zhai", "Xing-Wei Liao", "Yu-Chao Liu", "Shi-Hua Yin"], "journal": "Journal of oncology", "year": 2020, "abstract": "Neurofibromatosis Type 2- (NF2-) associated vestibular schwannomas (VSs) are histologically benign tumors. This study aimed to determine disease-related genes, pathways, and potential therapeutic drugs associated with NF2-VSs using the bioinformatics method. Microarray data of GSE108524 were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were screened using GEO2R. The functional enrichment and pathway enrichment of DEGs were performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes Genomes (KEGG). Furthermore, the STRING and Cytoscape were used to analyze the protein-protein interaction (PPI) network of all differentially expressed genes and identify hub genes. Finally, the enriched gene sets belonging to the identified pathways were queried against the Drug-Gene Interaction database to find drug candidates for topical use in NF2-associated VSs. A total of 542 DEGs were identified, including 13 upregulated and 329 downregulated genes, which were mainly enriched in terms of focal adhesion, PI3K-Akt signaling pathway, ECM-receptor interaction, Toll-like receptor signaling pathway, Rap1 signaling pathway, and regulation of actin cytoskeleton. 28 hub genes were identified based on the subset of PPI network, and 31 drugs were selected based on the Drug-Gene Interaction database. Drug discovery using bioinformatics methods facilitates the identification of existing or potential therapeutic drugs to improve NF2 treatment.", "claims": [{"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32733557", "locator": "sections[19] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32733557"], "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. 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Functional Annotation and Pathway Enrichment Analysis of DEGs", "row_count": 29, "column_count": 4}, "table": {"label": "Table 2", "caption": "KEGG pathway analysis of differentially expressed genes.", "rows": [["Term", "Count", "P value", "Genes"], ["hsa05150: staphylococcus aureus infection", "13", "<0.001", "C3AR1, C3, HLA-DRB3, FPR1, C1R, C1S, HLA-DQA1, FCGR1A, CFH, FCGR3A, CFD, SELPLG, FCGR3B"], ["hsa04145: phagosome", "19", "<0.001", "MRC1, NOS1, OLR1, C3, TUBB2A, HLA-DRB3, TLR2, HLA-C, C1R, TLR6, HLA-DQA1, CYBB, CD36, FCGR1A, COMP, CLEC7A, FCGR3A, FCGR3B, THBS4"], ["hsa04514: cell adhesion molecules (CAMs)", "16", "<0.001", "CLDN19, HLA-DRB3, HLA-C, L1CAM, NLGN3, CDH2, HLA-DQA1, CDH5, ALCAM, NCAM1, CD86, CD34, ITGA8, CLDN1, CD4, SELPLG"], ["hsa04640: hematopoietic cell lineage", "12", "<0.001", "CR1, CD37, CD36, CD34, HLA-DRB3, FCGR1A, MME, IL1B, CD4, ANPEP, CSF2RA, CSF1R"], ["hsa05144: malaria", "9", "<0.001", "CR1, CD36, COMP, TLR2, IL1B, HBA2, HBA1, HBB, THBS4"], ["hsa04610: complement and coagulation cascades", "10", "<0.001", "C3AR1, VWF, CR1, C3, F13A1, CFH, TFPI, C1R, C1S, CFD"], ["hsa04510: focal adhesion", "17", "0.0017", "PIK3CG, EGFR, CAV1, TNXB, TNC, FLNB, MYL9, VWF, CCND1, PAK3, CCND2, COMP, ITGA8, COL6A3, PDGFRA, SPP1, THBS4"], ["hsa04060: cytokine-cytokine receptor interaction", "18", "0.0022", "EGFR, CCL3, TGFBR1, LIFR, EDA2R, CCL4L1, CCL4, CXCL12, IL17RA, LEP, PPBP, CXCL14, CCL3L3, CX3CR1, PDGFRA, IL1B, CSF2RA, CSF1R"], ["hsa05140: leishmaniasis", "9", "0.0027", "CR1, C3, HLA-DRB3, FCGR1A, TLR2, IL1B, FCGR3A, FCGR3B, HLA-DQA1"], ["hsa04151: PI3K-akt signaling pathway", "23", "0.0033", "EGFR, PIK3CG, FGF7, TNXB, TNC, TLR2, FGF10, IRS1, DDIT4, VWF, CCND1, LPAR5, CCND2, COMP, ITGA8, COL6A3, PDGFRA, MDM2, ANGPT1, FGF1, SPP1, THBS4, CSF1R"], ["hsa00350: tyrosine metabolism", "6", "0.0063", "MAOA, AOX1, ADH1C, ADH1B, ADH1A, AOC3"], ["hsa03320: PPAR signaling pathway", "8", "0.0075", "LPL, CD36, OLR1, PLIN1, SLC27A6, FABP4, ACADL, ADIPOQ"], ["hsa04512: ECM-receptor interaction", "9", "0.0094", "VWF, CD36, TNXB, COMP, TNC, ITGA8, COL6A3, SPP1, THBS4"], ["hsa04620: Toll-like receptor signaling pathway", "10", "0.0100", "PIK3CG, CD86, CCL3, CCL3L3, TLR2, CCL4L1, IL1B, TLR6, CCL4, SPP1"], ["hsa05323: rheumatoid arthritis", "9", "0.0101", "CD86, CCL3, HLA-DRB3, CCL3L3, TLR2, IL1B, ANGPT1, CXCL12, HLA-DQA1"], ["hsa05218: melanoma", "8", "0.0103", "PIK3CG, EGFR, CCND1, FGF7, PDGFRA, MDM2, FGF10, FGF1"], ["hsa04015: Rap1 signaling pathway", "15", "0.0126", "FYB, PIK3CG, EGFR, FGF7, FPR1, FGF10, APBB1IP, DOCK4, PLCB4, LPAR5, RASGRP3, PDGFRA, ANGPT1, FGF1, CSF1R"], ["hsa05416: viral myocarditis", "7", "0.0126", "CAV1, CD86, CCND1, HLA-DRB3, SGCD, HLA-C, HLA-DQA1"], ["hsa04730: long-term depression", "7", "0.0160", "PLA2G4A, PLCB4, NOS1, GRIA2, LYN, GUCY1A2, GUCY1B3"], ["hsa05206: microRNAs in cancer", "18", "0.0176", "EGFR, TNXB, CYP1B1, TNC, MIRLET7F1, MIR99A, ZEB1, MIR222, MIR221, IRS1, DDIT4, NOTCH3, CCND1, CCND2, PDGFRA, MDM2, MARCKS, MIR181B2"], ["hsa05152: tuberculosis", "13", "0.0178", "MRC1, CR1, ITGAX, C3, FCGR1A, HLA-DRB3, TLR2, IL1B, CLEC7A, FCGR3A, TLR6, FCGR3B, HLA-DQA1"], ["hsa05205: proteoglycans in cancer", "14", "0.0191", "PIK3CG, EGFR, CAV1, LUM, FZD1, TLR2, DCN, FLNB, CCND1, CBLB, GPC3, RRAS2, MDM2, PTCH1"], ["hsa05143: African trypanosomiasis", "5", "0.0250", "PLCB4, IL1B, HBA2, HBA1, HBB"], ["hsa05332: graft-versus-host disease", "5", "0.0250", "CD86, HLA-DRB3, IL1B, HLA-C, HLA-DQA1"], ["hsa05142: Chagas disease (American trypanosomiasis)", "9", "0.0254", "PIK3CG, CCL3, PLCB4, C3, TGFBR1, CCL3L3, TLR2, IL1B, TLR6"], ["hsa05200: pathways in cancer", "22", "0.0267", "EGFR, PIK3CG, FGF7, TGFBR1, FZD1, RUNX1T1, FGF10, CXCL12, CBLB, CCND1, PLCB4, LPAR5, RASGRP3, SLC2A1, PDGFRA, MDM2, PTCH1, PTCH2, HHIP, FGF1, CSF2RA, CSF1R"], ["hsa04810: regulation of actin cytoskeleton", "14", "0.0282", "PIK3CG, EGFR, FGF7, FGF10, NCKAP1L, MYL9, ARPC1B, ITGAX, CHRM3, PAK3, ITGA8, RRAS2, PDGFRA, FGF1"], ["hsa04380: osteoclast differentiation", "10", "0.0349", "PIK3CG, CYBB, FCGR1A, TGFBR1, IL1B, FCGR3A, TREM2, FCGR3B, CSF1R, BLNK"]], "row_count": 29, "column_count": 4, "numeric_cells": 102, "header_rows": 1, "locator": "section[13]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:32733557:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9d3a21b08782ea5be2219e4ee6b46ec0689075062d46d05a067815ddb5e4b738", "bytes": 952, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab3", "version": null, "note": "28 hub genes with connectivity degree ≥20.", "structure": {"pmcid": "PMC7378604", "section_index": 14, "section_title": "3.3. 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