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Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network.
[esophageal squamous cell carcinoma]
The
aim
of
this
study
was
to
identify
the
candidate
genes
of
esophageal
squamous
cell
carcinoma
(
ESCC
)
.
Gene
expression
profiling
of
17
ESCC
samples
and
17
adjacent
normal
samples
,
GSE
20347
,
was
downloaded
from
Gene
Expression
Omnibus
database
.
The
raw
data
were
preprocessed
,
and
the
differentially
expressed
genes
(
DEGs
)
between
ESCC
and
normal
samples
were
identified
by
using
SAM
software
(
false
discovery
rate
<
0
.
001
)
.
Then
,
the
co
-expression
network
of
DEGs
was
constructed
based
on
Pearson
's
correlation
test
(
r-value
≥
0
.
8
)
.
Furthermore
,
the
topological
properties
of
the
co
-expression
network
were
analyzed
through
NetworkAnalyzer
(
default
settings
)
of
Cytoscape
.
The
expression
fold
changes
of
DEGs
and
topological
properties
were
utilized
to
identify
the
candidate
genes
of
ESCC
(
Crin
score
>
4
)
,
which
were
further
analyzed
based
on
DAVID
functional
enrichment
analysis
(
P-
value
<
0
.
05
)
.
A
total
of
1
,
063
DEGs
were
identified
,
including
490
up-regulated
and
573
down-regulated
DEGs
.
Then
,
the
co
-expression
network
of
DEGs
was
constructed
,
containing
999
nodes
and
46
,
323
edges
.
Based
on
the
expression
fold
changes
of
DEGs
and
the
topological
properties
of
the
co
-expression
network
,
DEGs
were
ranked
,
and
the
top
24
genes
were
candidate
genes
of
ESCC
,
such
as
CRISP
3
,
EREG
,
CXCR
2
,
and
CRNN
.
Furthermore
,
the
24
genes
were
significantly
enriched
in
bio-functions
regarding
cell
differentiation
,
glucan
biosynthetic
process
and
immune
response
.
The
present
study
suggested
that
CRISP
3
,
EREG
,
CXCR
2
,
and
CRNN
might
be
causative
genes
of
ESCC
,
and
play
vital
roles
in
the
development
of
ESCC
.
However
,
further
experimental
studies
are
needed
to
confirm
our
results
.
Diseases
Validation
Diseases presenting
"gse20347"
symptom
esophageal squamous cell carcinoma
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