Download cn

B. How to use
e Parametriic Analysis o
of Gene Sett Enrichmen
nt (PAGE)? PAGE method is argued by Kim
m [BMC Bioin
nformatics 20
005, 6:144]. U
Using Central Limit Theore
em in statiistics, this method m
is sim
mple and effiicient. Differe
ent to SEA, it takes exprression level into acco
ount, and can
n deal with a llong list of geenes/probese
ets. STEP
P 1: Firsttly, you should choose the species forr your query data. Pleasee make sure tthat identifie
ers in yourr input should be one of datatypes in
nside the righ
ht information table. If yo
our identifiers are not stored in agrriGO, there iss another tw
wo ways: one is provided your own GO
O annotation
n file, the o
other is to usse our BLAST4
4ID service.
P 2: STEP
In PA
AGE analysis,, user should pay more atttention to inp
put data. As p
presented in the followingg imagge, as least tw
wo rows must be provided
d. The first ro
ow is sequencce identifiers,, and followin
ngs are n
numerical value. The num
merical value iis fold change
e (FC) or log2
2‐transformed
d FC value (laatter prefferred) of thee identifiers' eexpression un
nder differentt condition. Iff you do not have expresssion dataa, then SEA m
may be the altternative choice. In aggriGO’s exam
mple, there are 3 rows in th
his example. First row is A
ATH1 probeseet name, the seco
ond row is expression fold change (FC) value of cold
d treatment to CK(cold/CK
K) after half hour. Third
d row is exprression FC of cold/CK afterr 24 hour cold
d treatment. Only 600 pro
obesets are in
n the quicck example fo
or the fast loaad of the HTM
ML page. To o
obtain a full view of PAGE method, you
u can dow
wnload the fulll example filee and exploree the followin
ng analysis prrocedure.