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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
"squamous cell carcinoma"
symptom
carcinoma of the gallbladder
child syndrome
dystrophic epidermolysis bullosa
epidermolysis bullosa simplex
esophageal adenocarcinoma
esophageal carcinoma
esophageal squamous cell carcinoma
junctional epidermolysis bullosa
kallmann syndrome
kindler syndrome
liposarcoma
monosomy 21
oculocutaneous albinism
oral submucous fibrosis
papillon-lefèvre syndrome
This symptom has already been validated
