<s>
However	O
most	O
frequently	O
,	O
pathway	B-Application
analysis	I-Application
refers	O
to	O
a	O
method	O
of	O
initial	O
characterization	O
and	O
interpretation	O
of	O
an	O
experimental	O
(	O
or	O
pathological	O
)	O
condition	O
that	O
was	O
studied	O
with	O
omics	O
tools	O
or	O
genome-wide	O
association	O
study	O
.	O
</s>
<s>
The	O
data	O
for	O
pathway	B-Application
analysis	I-Application
come	O
from	O
high	O
throughput	O
biology	O
.	O
</s>
<s>
Before	O
pathway	B-Application
analysis	I-Application
can	O
be	O
done	O
,	O
each	O
gene	O
's	O
alteration	O
should	O
be	O
evaluated	O
using	O
the	O
omics	O
dataset	O
in	O
either	O
quantitative	O
(	O
differential	O
expression	O
analysis	O
)	O
or	O
qualitative	O
(	O
detection	O
of	O
somatic	O
point	O
mutations	O
or	O
mapping	O
neighbor	O
genes	O
to	O
a	O
disease-associated	O
SNP	O
)	O
.	O
</s>
<s>
Further	O
,	O
a	O
list	O
where	O
gene	O
identifiers	O
are	O
accompanied	O
by	O
the	O
alteration	O
attributes	O
is	O
subjected	O
to	O
a	O
pathway	B-Application
analysis	I-Application
.	O
</s>
<s>
By	O
using	O
pathway	B-Application
analysis	I-Application
software	O
,	O
researchers	O
can	O
determine	O
which	O
s	O
are	O
enriched	O
with	O
the	O
altered	O
experimental	O
genes	O
For	O
example	O
,	O
pathway	B-Application
analysis	I-Application
of	O
several	O
independent	O
microarray	O
experiments	O
(	O
meta-analysis	O
)	O
helped	O
to	O
discover	O
potential	O
biomarkers	O
in	O
a	O
single	O
pathway	O
important	O
for	O
fast-to-slow	O
switch	O
fiber	O
type	O
transition	O
in	O
Duchenne	O
muscular	O
dystrophy	O
.	O
</s>
<s>
Pathway	O
collections	O
and	O
interaction	O
networks	O
constitute	O
the	O
knowledge	O
base	O
required	O
for	O
a	O
pathway	B-Application
analysis	I-Application
.	O
</s>
<s>
Pathway	O
Studio	O
and	O
Ingenuity	O
Pathway	B-Application
Analysis	I-Application
tools	O
.	O
</s>
<s>
Pathway	B-Application
analysis	I-Application
software	O
can	O
be	O
found	O
in	O
the	O
form	O
of	O
desktop	O
programs	O
,	O
web-based	O
applications	O
,	O
or	O
packages	O
coded	O
in	O
such	O
languages	O
as	O
R	B-Language
and	O
Python	B-Language
and	O
shared	O
openly	O
through	O
the	O
BioConductor	B-Application
and	O
GitHub	B-Application
projects	O
.	O
</s>
<s>
The	O
methodology	O
of	O
pathway	B-Application
analysis	I-Application
evolves	O
fast	O
and	O
the	O
classification	O
is	O
still	O
discussable	O
,	O
with	O
the	O
following	O
main	O
categories	O
of	O
pathway	O
enrichment	O
analysis	O
applicable	O
to	O
high-throughput	O
data	O
:	O
</s>
<s>
The	O
aim	O
of	O
ORA	O
is	O
to	O
identify	O
such	O
enriched	O
pathways	O
,	O
judging	O
by	O
statistical	B-General_Concept
significance	I-General_Concept
of	O
the	O
overlap	O
between	O
FGS	O
and	O
AGS	O
as	O
determined	O
either	O
by	O
an	O
appropriate	O
statistic	O
,	O
such	O
as	O
Jaccard	O
index	O
or	O
by	O
a	O
statistical	O
test	O
producing	O
p-values	O
(	O
Fisher	B-General_Concept
's	I-General_Concept
exact	I-General_Concept
test	I-General_Concept
or	O
the	O
test	O
using	O
hypergeometric	O
distribution	O
)	O
.	O
</s>
<s>
This	O
full	O
list	O
should	O
be	O
therefore	O
ranked	O
in	O
advance	O
by	O
a	O
statistic	O
(	O
such	O
as	O
mRNA	O
expression	O
fold-change	O
,	O
Student	B-General_Concept
's	I-General_Concept
t-test	I-General_Concept
etc	O
.	O
)	O
</s>
<s>
Thus	O
FCS	O
takes	O
into	O
account	O
every	O
FGS	O
gene	O
regardless	O
of	O
its	O
statistical	B-General_Concept
significance	I-General_Concept
and	O
does	O
not	O
require	O
pre-compiled	O
.	O
</s>
<s>
Beyond	O
open-source	O
tools	O
,	O
such	O
as	O
STRING	O
or	O
Cytoscape	B-Language
,	O
a	O
number	O
of	O
companies	O
sell	O
licensed	O
software	O
products	O
to	O
analyse	O
gene	O
sets	O
.	O
</s>
<s>
Application	O
of	O
pathway	B-Application
analysis	I-Application
methods	O
depends	O
on	O
annotations	O
found	O
in	O
existing	O
databases	B-Application
,	O
such	O
as	O
gene	O
set	O
membership	O
in	O
pathways	O
,	O
pathway	O
topology	O
,	O
presence	O
of	O
genes	O
in	O
the	O
global	O
network	O
etc	O
.	O
</s>
<s>
Therefore	O
,	O
interpretation	O
of	O
pathway	B-Application
analysis	I-Application
results	O
for	O
omics	O
datasets	O
should	O
be	O
done	O
with	O
caution	O
Partially	O
,	O
the	O
problem	O
can	O
be	O
addressed	O
by	O
analysing	O
larger	O
gene	O
sets	O
in	O
a	O
more	O
,	O
such	O
as	O
big	O
pathway	O
collections	O
or	O
global	O
interaction	O
networks	O
.	O
</s>
