<s>
Weighted	B-Algorithm
correlation	I-Algorithm
network	I-Algorithm
analysis	I-Algorithm
,	O
also	O
known	O
as	O
weighted	O
gene	O
co-expression	O
network	O
analysis	O
(	O
WGCNA	B-Algorithm
)	O
,	O
is	O
a	O
widely	O
used	O
data	B-Application
mining	I-Application
method	O
especially	O
for	O
studying	O
biological	O
networks	O
based	O
on	O
pairwise	O
correlations	O
between	O
variables	O
.	O
</s>
<s>
While	O
it	O
can	O
be	O
applied	O
to	O
most	O
high-dimensional	B-Algorithm
data	O
sets	O
,	O
it	O
has	O
been	O
most	O
widely	O
used	O
in	O
genomic	O
applications	O
.	O
</s>
<s>
WGCNA	B-Algorithm
can	O
be	O
used	O
as	O
a	O
data	B-General_Concept
reduction	I-General_Concept
technique	I-General_Concept
(	O
related	O
to	O
oblique	O
factor	O
analysis	O
)	O
,	O
as	O
a	O
clustering	B-Algorithm
method	O
(	O
fuzzy	O
clustering	B-Algorithm
)	O
,	O
as	O
a	O
feature	B-General_Concept
selection	I-General_Concept
method	O
(	O
e.g.	O
</s>
<s>
as	O
gene	O
screening	O
method	O
)	O
,	O
as	O
a	O
framework	O
for	O
integrating	O
complementary	O
(	O
genomic	O
)	O
data	O
(	O
based	O
on	O
weighted	O
correlations	O
between	O
quantitative	O
variables	O
)	O
,	O
and	O
as	O
a	O
data	B-General_Concept
exploratory	I-General_Concept
technique	O
.	O
</s>
<s>
Although	O
WGCNA	B-Algorithm
incorporates	O
traditional	O
data	B-General_Concept
exploratory	I-General_Concept
techniques	O
,	O
its	O
intuitive	O
network	O
language	O
and	O
analysis	O
framework	O
transcend	O
any	O
standard	O
analysis	O
technique	O
.	O
</s>
<s>
By	O
selecting	O
intramodular	O
hubs	O
in	O
consensus	O
modules	O
,	O
WGCNA	B-Algorithm
also	O
gives	O
rise	O
to	O
network	O
based	O
meta	O
analysis	O
techniques	O
.	O
</s>
<s>
The	O
WGCNA	B-Algorithm
method	O
was	O
developed	O
by	O
Steve	O
Horvath	O
,	O
a	O
professor	O
of	O
human	O
genetics	O
at	O
the	O
David	O
Geffen	O
School	O
of	O
Medicine	O
at	O
UCLA	O
and	O
of	O
biostatistics	O
at	O
the	O
UCLA	O
Fielding	O
School	O
of	O
Public	O
Health	O
and	O
his	O
colleagues	O
at	O
UCLA	O
,	O
and	O
(	O
former	O
)	O
lab	O
members	O
(	O
in	O
particular	O
Peter	O
Langfelder	O
,	O
Bin	O
Zhang	O
,	O
Jun	O
Dong	O
)	O
.	O
</s>
<s>
Weighted	B-Algorithm
correlation	I-Algorithm
network	I-Algorithm
analysis	I-Algorithm
can	O
be	O
attractive	O
for	O
the	O
following	O
reasons	O
:	O
</s>
<s>
Resulting	O
network	O
statistics	O
can	O
be	O
used	O
to	O
enhance	O
standard	O
data-mining	B-Application
methods	O
such	O
as	O
cluster	B-Algorithm
analysis	I-Algorithm
since	O
(	O
dis	O
)	O
-similarity	O
measures	O
can	O
often	O
be	O
transformed	O
into	O
weighted	O
networks	O
;	O
see	O
chapter	O
6	O
in	O
.	O
</s>
<s>
WGCNA	B-Algorithm
provides	O
powerful	O
module	O
preservation	O
statistics	O
which	O
can	O
be	O
used	O
to	O
quantify	O
similarity	O
to	O
another	O
condition	O
.	O
</s>
<s>
Next	O
,	O
an	O
adjacency	B-Algorithm
matrix	I-Algorithm
(	O
network	O
)	O
,	O
,	O
is	O
used	O
to	O
quantify	O
how	O
strongly	O
genes	O
are	O
connected	O
to	O
one	O
another	O
.	O
</s>
<s>
Specifically	O
,	O
WGCNA	B-Algorithm
uses	O
the	O
following	O
power	O
function	O
assess	O
their	O
connection	O
strength	O
:	O
</s>
<s>
Since	O
this	O
soft-thresholding	O
procedure	O
applied	O
to	O
a	O
pairwise	O
correlation	O
matrix	O
leads	O
to	O
weighted	O
adjacency	B-Algorithm
matrix	I-Algorithm
,	O
the	O
ensuing	O
analysis	O
is	O
referred	O
to	O
as	O
weighted	O
gene	O
co-expression	O
network	O
analysis	O
.	O
</s>
<s>
Typically	O
,	O
WGCNA	B-Algorithm
uses	O
the	O
topological	O
overlap	O
measure	O
(	O
TOM	O
)	O
as	O
proximity	O
.	O
</s>
<s>
This	O
proximity	O
is	O
used	O
as	O
input	O
of	O
average	O
linkage	O
hierarchical	O
clustering	B-Algorithm
.	O
</s>
<s>
WGCNA	B-Algorithm
has	O
been	O
widely	O
used	O
for	O
analyzing	O
gene	O
expression	O
data	O
(	O
i.e.	O
</s>
<s>
Such	O
as	O
,	O
WGCNA	B-Algorithm
study	O
reveals	O
novel	O
transcription	O
factors	O
are	O
associated	O
with	O
Bisphenol	O
A	O
(	O
BPA	O
)	O
dose-response	O
.	O
</s>
<s>
It	O
is	O
often	O
used	O
as	O
data	B-General_Concept
reduction	I-General_Concept
step	O
in	O
systems	O
genetic	O
applications	O
where	O
modules	O
are	O
represented	O
by	O
"	O
module	O
eigengenes	O
"	O
e.g.	O
</s>
<s>
WGCNA	B-Algorithm
is	O
widely	O
used	O
in	O
neuroscientific	O
applications	O
,	O
e.g.	O
</s>
<s>
functional	B-Algorithm
MRI	I-Algorithm
data	O
.	O
</s>
<s>
R	B-Language
add-on	O
packages	O
.	O
</s>
