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pmid:30774816

Gene expression analysis of colon high-grade dysplasia revealed new molecular mechanism of disease.

Habib Malekpour · Mohammad Hossein Heidari · Reza Vafaee · Hamideh Moravvej Farshi · Mahsa Khodadoostan

Gastroenterology and hepatology from bed to bench · 2018

Paper

partial

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
sci_version
1.2
id
pmid:30774816
kind
science-record
revision
8
content_hash
sha256:6cfe58dacdf07ef90233f74504e632fd128c7438a9527a89b4358a90bd42c287
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:42Z
updated_at
2026-11-01T22:00:23Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
partial
title
Gene expression analysis of colon high-grade dysplasia revealed new molecular mechanism of disease.
doi
null
pmid
30774816
authors array · 5 items
[0]
Habib Malekpour
[1]
Mohammad Hossein Heidari
[2]
Reza Vafaee
[3]
Hamideh Moravvej Farshi
[4]
Mahsa Khodadoostan
journal
Gastroenterology and hepatology from bed to bench
year
2018
abstract
AIM: The aim of this research was to find a clear molecular view of dysplasia via network analysis. BACKGROUND: There are some evidence suggest the relationship between dysplasia and colorectal cancer. Understanding of high-grade dysplasia (HGD) could be beneficial for colon cancer management. METHODS: Bioinformatics study of HGD versus healthy subjects was conducted to check the status of differentially expressed genes (DEGs). GSE31106, GPL1261, GSM770092-94 and GSM770101-6 were the sources from gene expression omnibus (GEO) that queried for protein-protein interaction (PPI) network analysis via Cytoscape and its algorithms. Hubs of network were enriched for biochemical pathways and were validated via clustering analysis. RESULTS: Numbers of 46 hub nodes were determined and were included in 12 pathways. A main cluster including 76 nodes was identified containing 45 hubs. 33 hubs among 46 genes were involved in biochemical pathways. IL1B, IL6, TNF, and TRL4 were the most important critical genes. CONCLUSION: Many different genes as hub nodes might influence the trigger and development of advance condition and also colon cancer.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30774816
locator
sections[2] "Methods" paragraph 7
quote
Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30774816
locator
sections[2] "Methods" paragraph 3
quote
Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.
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complete
gaps array · 1 item
[0]
doi
experiment object · 8 fields
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complete
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null
steps array · 3 items
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read_published_estimate
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1
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Read the published estimate from the source
kind
other
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complete
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null
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The claim, method and evidence span published with the source article.
duration_hours
null
parameters object · 0 fields
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[0]
source:pmid:30774816
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[0]
the published estimate and its evidence
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obtain_source_data
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Obtain the source data from the named repository
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data-preparation
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complete
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null
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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
inputs array · 1 item
[0]
data:geo:GSE31106
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[0]
the source data with its repository provenance
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run_analysis
order
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Run the published analysis
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analysis
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complete
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null
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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:GSE31106
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[0]
the replicated result and its comparison
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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
PMC6347998
source
europe_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE31106
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raw
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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=GSE31106
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null
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null
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Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.
access_statement_kind
repository_route_statement
sample_accessions array · 18 items
[0]
GSM770092
[1]
GSM770093
[2]
GSM770094
[3]
GSM770095
[4]
GSM770096
[5]
GSM770097
[6]
GSM770098
[7]
GSM770099
[8]
GSM770100
[9]
GSM770101
[10]
GSM770102
[11]
GSM770103
[12]
GSM770104
[13]
GSM770105
[14]
GSM770106
[15]
GSM770107
[16]
GSM770108
[17]
GSM770109
sample_count
18
group_sizes
null
group_sizes_basis
null
platform
1261
taxon
Mus musculus
title
Expression data for the different phases of ulcerative colitis-associated carcinogenesis in a mouse model
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
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false
licence_read
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[2] object · 16 fields
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null
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Hub nodes of HGD network
structure object · 5 fields
pmcid
PMC6347998
section_index
3
section_title
Results
row_count
47
column_count
6
table object · 8 fields
label
Table 1
caption
Hub nodes of HGD network
rows array · 47 items
[0] array · 6 items
[0]
R
[1]
display name
[2]
Description
[3]
Degree
[4]
BC
[5]
CC
[1] array · 6 items
[0]
1
[1]
GAPDH
[2]
glyceraldehyde-3-phosphate dehydrogenase
[3]
67
[4]
0.059
[5]
0.706
[2] array · 6 items
[0]
2
[1]
IL6
[2]
interleukin 6 (interferon, beta 2)
[3]
64
[4]
0.021
[5]
0.677
[3] array · 6 items
[0]
3
[1]
TNF
[2]
tumor necrosis factor
[3]
63
[4]
0.025
[5]
0.673
[4] array · 6 items
[0]
4
[1]
INS
[2]
Insulin
[3]
63
[4]
0.058
[5]
0.681
[5] array · 6 items
[0]
5
[1]
TGFB1
[2]
transforming growth factor, beta 1
[3]
58
[4]
0.071
[5]
0.657
[6] array · 6 items
[0]
6
[1]
IL8
[2]
interleukin 8
[3]
58
[4]
0.026
[5]
0.653
[7] array · 6 items
[0]
7
[1]
ALB
[2]
Albumin
[3]
58
[4]
0.019
[5]
0.653
[8] array · 6 items
[0]
8
[1]
CCL2
[2]
chemokine (C-C motif) ligand 2
[3]
58
[4]
0.012
[5]
0.657
[9] array · 6 items
[0]
9
[1]
AKT1
[2]
v-akt murine thymoma viral oncogene homolog 1
[3]
58
[4]
0.046
[5]
0.661
[10] array · 6 items
[0]
10
[1]
VEGFA
[2]
vascular endothelial growth factor A
[3]
57
[4]
0.029
[5]
0.649
[11] array · 6 items
[0]
11
[1]
IL1B
[2]
interleukin 1, beta
[3]
56
[4]
0.024
[5]
0.646
[12] array · 6 items
[0]
12
[1]
JUN
[2]
jun proto-oncogene
[3]
56
[4]
0.021
[5]
0.661
[13] array · 6 items
[0]
13
[1]
PRDM10
[2]
PR domain containing 10
[3]
56
[4]
0.027
[5]
0.657
[14] array · 6 items
[0]
14
[1]
IL10
[2]
interleukin 10
[3]
54
[4]
0.009
[5]
0.638
[15] array · 6 items
[0]
15
[1]
IL4
[2]
interleukin 4
[3]
54
[4]
0.013
[5]
0.638
[16] array · 6 items
[0]
16
[1]
CSF2
[2]
colony stimulating factor 2 (granulocyte-macrophage)
[3]
54
[4]
0.012
[5]
0.638
[17] array · 6 items
[0]
17
[1]
MMP9
[2]
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)
[3]
53
[4]
0.005
[5]
0.631
[18] array · 6 items
[0]
18
[1]
TLR4
[2]
toll-like receptor 4
[3]
52
[4]
0.008
[5]
0.631
[19] array · 6 items
[0]
19
[1]
DECR1
[2]
2,4-dienoyl CoA reductase 1, mitochondrial
[3]
51
[4]
0.046
[5]
0.635
[20] array · 6 items
[0]
20
[1]
SRC
[2]
v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)
[3]
51
[4]
0.015
[5]
0.631
[21] array · 6 items
[0]
21
[1]
VCAM1
[2]
vascular cell adhesion molecule 1
[3]
51
[4]
0.009
[5]
0.628
[22] array · 6 items
[0]
22
[1]
NOS3
[2]
nitric oxide synthase 3 (endothelial cell)
[3]
50
[4]
0.028
[5]
0.628
[23] array · 6 items
[0]
23
[1]
TP53
[2]
tumor protein p53
[3]
49
[4]
0.051
[5]
0.632
[24] array · 6 items
[0]
24
[1]
CXCR4
[2]
chemokine (C-X-C motif) receptor 4
[3]
48
[4]
0.007
[5]
0.608
[25] array · 6 items
[0]
25
[1]
ITGAM
[2]
integrin, alpha M (complement component 3 receptor 3 subunit)
[3]
48
[4]
0.011
[5]
0.611
[26] array · 6 items
[0]
26
[1]
IL13
[2]
interleukin 13
[3]
48
[4]
0.008
[5]
0.611
[27] array · 6 items
[0]
27
[1]
IL17A
[2]
interleukin 17A
[3]
47
[4]
0.025
[5]
0.595
[28] array · 6 items
[0]
28
[1]
TLR2
[2]
toll-like receptor 2
[3]
47
[4]
0.014
[5]
0.604
[29] array · 6 items
[0]
29
[1]
MAPK1
[2]
mitogen-activated protein kinase 1
[3]
47
[4]
0.019
[5]
0.614
[30] array · 6 items
[0]
30
[1]
EGFR
[2]
epidermal growth factor receptor
[3]
46
[4]
0.047
[5]
0.604
[31] array · 6 items
[0]
31
[1]
F2
[2]
coagulation factor II (thrombin)
[3]
45
[4]
0.015
[5]
0.608
[32] array · 6 items
[0]
32
[1]
EGF
[2]
epidermal growth factor
[3]
45
[4]
0.012
[5]
0.604
[33] array · 6 items
[0]
33
[1]
CXCL12
[2]
chemokine (C-X-C motif) ligand 12
[3]
45
[4]
0.003
[5]
0.592
[34] array · 6 items
[0]
34
[1]
CD44
[2]
CD44 molecule (Indian blood group)
[3]
44
[4]
0.004
[5]
0.598
[35] array · 6 items
[0]
35
[1]
IL18
[2]
interleukin 18 (interferon-gamma-inducing factor)
[3]
43
[4]
0.003
[5]
0.579
[36] array · 6 items
[0]
36
[1]
CAT
[2]
Catalase
[3]
43
[4]
0.040
[5]
0.601
[37] array · 6 items
[0]
37
[1]
IGF1
[2]
insulin-like growth factor 1 (somatomedin C)
[3]
43
[4]
0.007
[5]
0.592
[38] array · 6 items
[0]
38
[1]
NOS2
[2]
nitric oxide synthase 2, inducible
[3]
43
[4]
0.014
[5]
0.598
[39] array · 6 items
[0]
39
[1]
SPP1
[2]
secreted phosphoprotein 1
[3]
41
[4]
0.021
[5]
0.577
[40] array · 6 items
[0]
40
[1]
MMP2
[2]
matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)
[3]
41
[4]
0.002
[5]
0.582
[41] array · 6 items
[0]
41
[1]
ITGAX
[2]
integrin, alpha X (complement component 3 receptor 4 subunit)
[3]
40
[4]
0.006
[5]
0.562
[42] array · 6 items
[0]
42
[1]
MYD88
[2]
myeloid differentiation primary response 88
[3]
39
[4]
0.032
[5]
0.562
[43] array · 6 items
[0]
43
[1]
CCR5
[2]
chemokine (C-C motif) receptor 5 (gene/pseudogene)
[3]
37
[4]
0.002
[5]
0.554
[44] array · 6 items
[0]
44
[1]
AGT
[2]
angiotensinogen (serpin peptidase inhibitor, clade A, member 8)
[3]
36
[4]
0.008
[5]
0.559
[45] array · 6 items
[0]
45
[1]
CCR2
[2]
chemokine (C-C motif) receptor 2
[3]
35
[4]
0.001
[5]
0.549
[46] array · 6 items
[0]
46
[1]
CXCR2
[2]
chemokine (C-X-C motif) receptor 2
[3]
34
[4]
0.001
[5]
0.538
row_count
47
column_count
6
numeric_cells
230
header_rows
1
locator
section[3]/table-wrap[1]#T1
[3] object · 16 fields
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asset:table:pmid:30774816:2
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read_table
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section[3]/table-wrap[2]#T2
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null
note
Hub nodes that are involved in the 12 pathways
structure object · 5 fields
pmcid
PMC6347998
section_index
3
section_title
Results
row_count
12
column_count
3
table object · 8 fields
label
Table 2
caption
Hub nodes that are involved in the 12 pathways
rows array · 12 items
[0] array · 3 items
[0]
R
[1]
Gene name
[2]
Number of relevant pathways
[1] array · 3 items
[0]
1
[1]
IL1B, IL6
[2]
11
[2] array · 3 items
[0]
2
[1]
TNF, TRL4
[2]
10
[3] array · 3 items
[0]
3
[1]
JUN
[2]
9
[4] array · 3 items
[0]
4
[1]
CXCL8, MPK1
[2]
8
[5] array · 3 items
[0]
5
[1]
TLR2, TGFB1
[2]
7
[6] array · 3 items
[0]
6
[1]
NOS2, MYD88, IL10
[2]
6
[7] array · 3 items
[0]
7
[1]
CCL2
[2]
5
[8] array · 3 items
[0]
8
[1]
CSF2, IL18, AKT1
[2]
4
[9] array · 3 items
[0]
9
[1]
ITGAM, VEGFA, IL17A, IL4
[2]
3
[10] array · 3 items
[0]
10
[1]
NOS3, VCAM1, IL13
[2]
2
[11] array · 3 items
[0]
11
[1]
EGF, EGFR, GAPDH, IGF1, INS, MMP2, MMP9, CXCL12, SPP1
[2]
1
row_count
12
column_count
3
numeric_cells
27
header_rows
1
locator
section[3]/table-wrap[2]#T2
gaps array · 2 items
[0]
asset:data:geo:GSE31106 not downloaded
[1]
asset:data:geo:GSE31106 licence not read
analysis object · 4 fields
state
partial
methods array · 2 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
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
[1] object · 10 fields
id
method-2
family
null
specific
null
label
Boxplot analysis
dsl_operations array · 0 items
missing_operations array · 0 items
expressible
null
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
verbatim
quote
Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings.
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
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
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 · 2 items
[0]
GSE31106
[1]
GSM770092-94 and GSM770101-6
resolved_accessions array · 1 item
[0]
GSE31106
statements array · 1 item
[0]
Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.
basis
The paper names GSE31106 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 · 4 items
[0]
source:pmid:30774816
[1]
data:geo:GSE31106
[2]
asset:table:pmid:30774816:1
[3]
asset:table:pmid:30774816:2
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Complete file 
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30774816", "kind": "science-record", "revision": 8, "content_hash": "sha256:6cfe58dacdf07ef90233f74504e632fd128c7438a9527a89b4358a90bd42c287", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:00:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Gene expression analysis of colon high-grade dysplasia revealed new molecular mechanism of disease.", "doi": null, "pmid": "30774816", "authors": ["Habib Malekpour", "Mohammad Hossein Heidari", "Reza Vafaee", "Hamideh Moravvej Farshi", "Mahsa Khodadoostan"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2018, "abstract": "AIM: The aim of this research was to find a clear molecular view of dysplasia via network analysis.\nBACKGROUND: There are some evidence suggest the relationship between dysplasia and colorectal cancer. Understanding of high-grade dysplasia (HGD) could be beneficial for colon cancer management.\nMETHODS: Bioinformatics study of HGD versus healthy subjects was conducted to check the status of differentially expressed genes (DEGs). GSE31106, GPL1261, GSM770092-94 and GSM770101-6 were the sources from gene expression omnibus (GEO) that queried for protein-protein interaction (PPI) network analysis via Cytoscape and its algorithms. Hubs of network were enriched for biochemical pathways and were validated via clustering analysis.\nRESULTS: Numbers of 46 hub nodes were determined and were included in 12 pathways. A main cluster including 76 nodes was identified containing 45 hubs. 33 hubs among 46 genes were involved in biochemical pathways. IL1B, IL6, TNF, and TRL4 were the most important critical genes.\nCONCLUSION: Many different genes as hub nodes might influence the trigger and development of advance condition and also colon cancer.", "claims": [{"id": "claim-method", "statement": "Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774816", "locator": "sections[2] \"Methods\" paragraph 7", "quote": "Gene expression profiles were matched via boxplot analysis and p-value <0.05 was considered for significant findings."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774816", "locator": "sections[2] \"Methods\" paragraph 3", "quote": "Microarray Data (GSE31106, GPL1261, GSM770092-94 and GSM770101-6) were considered to compare Gene expression profiles of normal group and treated five-week-old male mice with intraperitoneal injected with 10mg/kg Azoxymethane."}], "state": "complete"}], "gaps": ["doi"]}, "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:30774816"], "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:GSE31106"], "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:GSE31106"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30774816", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:855ebcfc9f6933d579a6b0ac756e06b3904011e606dfe0b7ea48ecd33200fa5b", "bytes": 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