Glaab, Enrico and Baudot, Anais and Krasnogor, Natalio and

Glaab, Enrico and Baudot, Anais and Krasnogor, Natalio
and Valencia, Alfonso (2010) TopoGSA: network
topological gene set analysis. Bioinformatics, 26 (9). pp.
1271-1272. ISSN 1367-4803
Access from the University of Nottingham repository:
http://eprints.nottingham.ac.uk/1423/1/topogsa_manuscript_postprint.pdf
Copyright and reuse:
The Nottingham ePrints service makes this work by researchers of the University of
Nottingham available open access under the following conditions.
This article is made available under the University of Nottingham End User licence and may
be reused according to the conditions of the licence. For more details see:
http://eprints.nottingham.ac.uk/end_user_agreement.pdf
A note on versions:
The version presented here may differ from the published version or from the version of
record. If you wish to cite this item you are advised to consult the publisher’s version. Please
see the repository url above for details on accessing the published version and note that
access may require a subscription.
For more information, please contact [email protected]
0121345678
9
19121
187889
7
*
.
*.
!
"
$
%&
'
(
)
!
+
)
,
%
("
/
%
0
1
#
2
34/567')1311!+))-46891%):!;'11567'%!+))-46!8,
<3)
')'&-:(&67')-=-6!5+>?!@((!37
5A40B5C0
4DEE6 F73" % G1H77) (1()1( ) )41
67'))(9%'I)/1)GJ)7-771)1%/
-11(7)1%1)%61')1)1)GJ%KL//11)
)7-4)1%)%!%'4%)411)):/(1%)41
1)GJ)41)1(1:)/6 '%)1%!167')1((
671())4%1/JG1'7)4G:%(71%%1%K
5MN96/11:91)4))7OPPGGGK/)%K1)P)7-%
C179961K-Q%K))KK'J
R ST0BUVWC0SUT
\^\jbYe`^_ibi]ibZ\]}bfg\^[^ce_fbi]llbfbZ\gYm~gb\g^labZbgrbnan®Ye~
fbaY`_\bi¯hgn®i^kZ~fbaY`_\bi¯abZbg|n
sl\bfgYmc]\\]Za\jb`]g\^l]ibZ\]}bfgp\jb_ee`][_\]^Zc_eg\jbc^Z\^_Z
]Z\bf_[\]^ZZb\k^f‚rgbbceb̀cbZ\_\]^Zgb[\]^Z|p_Zi[^ceY\bg\^e^`^a][_`
ef^ebf\]bgl^f\jbbZ\]fbZb\k^f‚p\jbYe`^_ibiabZb°ef^\b]Zgb\_Zif_Zi^c
gb\g^lc_\[jbig]±bgnojb_h_]`_mb̀Zb\k^f‚\^e^`^a][_`ef^ebf\]bg_fb²
³ojb´tµ¶tt^l_Z^ibrabZb^fef^\b]Z|]g\jb_hbf_abZYcmbf^lbiabg
r]Z\bf_[\]^Zg|]Z[]ibZ\\^\j]gZ^ibn
³ojbw·¸vw¸w¹ºut¶»¼µ¸·t½¾¸»t¼u¬Y_Z\]}bg\jbef^m_m]`]\q\j_\\jb
Zb]ajm^Yfg^l_Z^ib_fb[^ZZb[\birgbb¿_\\gÀƒ\f^a_\±r†{{€||n
³ojbºÁ·¶utºuÂvuÁwt¼µuÁrƒÃÄ|l^f\k^Z^ibgÅÆ _ZiÅÇ ]Z_Z
YZi]fb[\bipYZkb]aj\biZb\k^f‚]gib}Zbi_g\jbc]Z]cYcZYcmbf^l
biabgkj][jj_hb\^mb\f_hbfgbi\^fb_[jÅÇlf^cÅÆn¿bYgb\jbƒÃÄ
_g_[bZ\f_`]\qcb_gYfbp[^ceY\]Za\jb_hbf_abƒÃÄlf^cb_[jZ^ib^l
]Z\bfbg\\^_``^\jbfZ^ibg]Z\jbZb\k^f‚n
³ojb¼·´tÈtuÉtt¼¼tººÊËÅÌ^l_Z^ibÅ[_Zmb[_`[Y`_\bilf^c\jb
ZYcmbf^lgj^f\bg\e_\jgÍÎÏlf^cZ^ibgÐ\^Ña^]Za\jf^YajŲ
ÍÎÏËÅÌ
ÊËÅÌÒ Ó
r†|
ÎÕÔÖ×ÎÔÕÏ×ÖÔÕÏØÙ ÍÎÏ
³ojbt»µt¼Út¸u·¶¸t¼u¶vw»uÛcb_gYfbg\jb]ce^f\_Z[b^lZb\k^f‚Z^ibg
mq_eeq̀]Za_[bZ\f_`]\qib}Z]\]^Zp]Zkj][j\jbg[^fb^lb_[j
Z^ibfb[]ef^[_`q̀ibebZig^Z\jbg[^fbg^l]\gZb]ajm^Yfgnª^fb
efb[]gbq̀p\jb[bZ\f_`]\qg[^fbg_fba]hbZmq\jbbZ\f]bg^l\jbi^c]Z_Z\
b]abZhb[\^f^l\jbZb\k^f‚_iÜ_[bZ[qc_\f]drgbbÝ^Z_[][jtuvwxryzz†|
l^f_ib\_]b̀ii]g[Ygg]^Z^l\j]gef^ebf\q|n
XYf\jbfc^fbpYgbf~ib}Zbiy§_ZiÞ§fbefbgbZ\_\]^Zg[_Zmbi]ge`_qbi
l^fb_[j]Zi]h]iY_`abZb°ef^\b]Z]Z\jbi_\_gb\_Zie`^\\bii_\_e^]Z\g_fb
]Z\bf`]Z‚bik]\jfbb̀h_Z\bZ\f]bg]Z_Z^Z`]Zb_ZZ^\_\]^Zi_\_m_gbn
XYZ[\]^Z_`abZ^c][bdebf]cbZ\gef^h]ibfbgb_f[jbfgk]\j_kb_`\j
^l]Zl^fc_\]^Zib`]Zb_\]ZaabZbgb\g^lm]^`^a][_`]Z\bfbg\no^
]Z\bfefb\\jbgb`]g\g^labZbgp[^cc^Zg\beg]Z_lYZ[\]^Z_`abZb
gb\_Z_q̀g]g]Z[Ỳib\jbgb_f[jl^fbZf][jcbZ\e_\\bfZgrl^f_fbh]bkp
gbbsm_\_Zab`^tuvwxryzz{||pbnan\^]ibZ\]lqg]aZ]}[_Z\g]aZ_``]Za
e_\jk_qg^fef^\b]Zi^c_]Zgp_Zi\bd\~c]Z]Za^l\jb`]\bf_\Yfb
rgbbfbh]bkmqf_``]Zabftuvwxryzz€||nsZ^\jbf_eef^_[jl^f\jb
lYZ[\]^Z_`]Z\bfefb\_\]^Z^labZbgb\g]g\jb_Z_q̀g]g^lc^b̀[Y`_f
]Z\bf_[\]^Zg]Zkj][j\jbabZbg^f\jb]f[^ffbge^Zi]Zaef^\b]Zg_fb
]Zh^h̀bip]Ze_f\][Y`_fef^\b]Z~ef^\b]Z]Z\bf_[\]^ZgnZ\j]g[^Z\bd\p
g^cbbd]g\]Zam]^]Zl^fc_\][g\^^g̀_f̀b_iq_``^kYgbfg\^c_eabZbg
^Z\^Zb\k^f‚g^l]Z\bf_[\]Za^flYZ[\]^Z_`q̀_gg^[]_\bic^b̀[Yb̀g\^
]ibZ\]lqfb`_\biabZbg_Zief^\b]ZgrƒZb`tuvwxpyzzz„…bZggbZtuvwxp
yzz†|n‡^kbhbfp\^\jbmbg\^l\jb_Y\j^fgˆ‚Z^kb̀iabpg^l_f\jbgb
\^^g̀i^Z^\\_‚b]Z\^_[[^YZ\\^e^`^a][_`ef^ebf\]bg]Z]Z\bf_[\]^Z
Zb\k^f‚g\^_Z_q̀gb_Zi[^ce_fbabZbgb\gn
Z\j]ge_ebfkb]Z\f^iY[bo^e^‰ƒsro^e^`^aq~m_gbi‰bZbƒb\
sZ_q̀g]g|p_kbm~\^^`\^h]gY_`]gb_Zi[^ce_fbZb\k^f‚\^e^`^a][_` ’“’ ߜࣗ¡›šœ– ›Ÿá¢–œ –¤ž–žšžŸš
ef^ebf\]bg^labZb^fef^\b]Zgb\gc_eebi^Z\^]Z\bf_[\]^ZZb\k^f‚gn ojb_Z_q̀g]g^lZb\k^f‚\^e^`^a][_`ef^ebf\]bg^l^Zq̀_g]Zab̀abZb°ef^\b]Z
Š ‹UBŒŽU‹ 5TV0‘UV4
’“” •–—˜™š›šœ–žŸ œ¡¢Ÿœ£œ˜œ¤›¥—˜£¡œ£ž¡Ÿ›žš
sZ_Z_q̀g]gmba]Zgk]\j\jbYe`^_i^l_`]g\^labZb^fef^\b]Z]ibZ\]}bfg
r¦Zgbcm`§gp‡‰¨©gqcm^g̀pb\[n„gbbkbme_abl^f_[^ceb̀\b`]g\^l
gYee^f\bil^fc_\g|ns`\bfZ_\]hbq̀p_c][f^_ff_qi_\_gb\[_ZmbYgbi_g
]ZeY\_Zii]llbfbZ\]_`q̀bdefbggbiabZbgk]``mbbd\f_[\bi_Y\^c_\][_`q̀
Yg]Zacb\j^iglf^c_efbh]^Ygq̀eYm`]gjbi^Z`]Zbc][f^_ff_q_Z_q̀g]g\^^`
r_ff_qc]Z]ZanZb\p‰`__mtuvwxryzz{||nª^fb^hbfp\jbYgbf[_Z_ii`_mbg̀
«\jbgb_Y\j^fg[^Z\f]mY\bib¬Y_`q̀\^\j]gk^f‚
­\^kj^c[^ffbge^ZibZ[bgj^Yìmb_iifbggbi
gb\i^bgZ^\b̀Zi]\gbl̀\^i]fb[\lYZ[\]^Z_`]Z\bfefb\_\]^Zn‡^kbhbfp
o^e^‰ƒsbZ_mb̀g\jbYgbf\^[^ce_fb\jbef^ebf\]bg^l_i_\_gb\^l]Z\bfbg\
\^_cY`\]\Yib^lefb~ib}Zbii_\_gb\g[^ffbge^Zi]Za\^‚Z^kZlYZ[\]^Z_`
ef^[bggbglf^c eYm`][i_\_m_gbgnX^f\jbjYc_Zgeb[]bgp\jbgb]Z[Ỳib
g]aZ_``]Zae_\jk_qgr¦‰‰p_Zbj]g_tuvwxryzzâ|pÝ]^©_f\_p¨]gj]cYf_
ryzz†||p‰bZbãZ\^`^aqrÝ]^`^a][_`Ãf^[bggpª^b̀[Y`_fXYZ[\]^Z_Zi
©b`Ỳ`_f©^ce^ZbZ\psgjmYfZbftuvwxryzzz||_ZiZ\bfÃf^ef^\b]Zi^c_]Zg
rsekb]b̀ftuvwxpyzz†|nƒYcc_f]bg^lZb\k^f‚\^e^`^a][_`ef^ebf\]bg_fb
ef^h]ibil^f_``abZb°ef^\b]Zgb\gp_Zi]Z\jby§_ZiÞ§e`^\gi]llbfbZ\
[^`^Yfgi]g\]ZaY]gji]llbfbZ\i_\_gb\gnägbfg[_Z]ibZ\]lqe_\jk_qg_Zi
ef^[bggbgg]c]`_f\^\jbYe`^_ibii_\_gb\h]gY_`q̀pm_gbi^Z\jbe`^\g^fm_gbi
^Z_\_mY`_ff_Z‚]ZaYg]Za_ZYcbf][_`g[^fb\^¬Y_Z\]lq\jbg]c]`_f]\q_[f^gg
_``\^e^`^a][_`ef^ebf\]bgnojbg]c]`_f]\qg[^fb]g^m\_]Zbimq[^ceY\]Za
åf_Z‚gl^fb_[je_\jk_q°ef^[bgggb\_[[^fi]Za\^\jb_mg^Ỳ\bi]llbfbZ[bg
mb\kbbZb_[j^l]\gåcbi]_Z\^e^`^a][_`ef^ebf\]bg_Zi\jb[^ffbge^Zi]Za
R
012234521
+,,1.DXJRN*J%&'()D+,,-.!B!*X]5 %&'()D+,,-..
!!F3 !#!! #0!"!JBK
YBK3!!!03#!#!!
*0!3K!!6!D3
2!F!!!JBKYB! 3!!^N_!!"./F!"!
!5!!"3ZMZ+!!M``La!!/!#D
!!!!53"!#*/0.D
b#*N/!".D *I/"!.!!*/!.0
! !""#3!!5!
QRBN*5%&'()D+,,E.!*
K!!"3!!!5./
##!"!#
0!!!!3!"!/Y0D
!!!5/0!!!!
K0!^_K!!"/
6789
9 !!"! :cd>We=8fg8;8>V
#$%&'()*+,,-../."! !!0*1.!*+.2 ."!! 5 # YKI #K"K!!"
"hYKIK+,,-K,,aLZaiDQ!"#!Q"
!3!*4./
!RI!hQQH$,1`LL[H1i!!Y!#3
!!!hQBj+,,aKEE`LLi/Q #C!
03/ 3!5" I0K3/
!!!6!" !,!1/
7 89:;<=8:>:=?@A@
B !!!! #"!5!!
! !0 "0" ! " !
!!!5!!*C!!%&'()D+,,E./
0!!F # !#3
3"!!# 5!! ! !*$%&'()
*+,,-.DGHH/!"//5H"!HIJHI!./!"!
!00!!!#!!D!0"D!
K6!3!5!*33!3
!1L!0!31,!!./$D
!#0!"!"!
!5*!30"!.!
!"!36!#!!!
!!!5*$"1.3./MN#!"!
!!D"!!"0!
LMO*JLM.!!"!5"/
P!!"!5"3!!
#3 4 D!!"!0
#"!*$"1.D!!0
!504!
!0!!!3!!"#*!"4K
QRB##D4!%&'()*+,,E.D$"1D!
!.D##333 K#
*$"1D#./B!!"#D"!5"
3!"!!"!!!"
0!!!!"*S"!T4!6D+,,-.D#33
33K4#*$"1D"!./
U A;<=8;8>V:VAW>
!5 !#! "!!" ! ! "!"!""R!K!3!JXJ/ !
!!!!5D!3 L
*YBJ*Y%&'()D1ZZZ.DNBJ*[!%&'()D+,,,.DQB\N*Q%&'()D
’
k8l8k8>c8@
!"Dm/%&'()*+,,Z.I0#3"!!!/nop
nqrqstruv'&qwxy
z*1.D+aL/
DR/%&'()*+,,1.B!JD!!"!!
3!3D!!3!!/{|w(%qw}wq~x%xy€*1.DMa/
!DY/%&'()*+,,,.!j!"#G3!F!3 "#/{'&
‚%s%&y€ƒD+L„+Z/
QD/%&'()*+,,1.QB\N„ !!!5/{|w(%qw
}wq~x%xy€*1.D+-+„+-L/
Q!DJ/%&'()*+,,1."!0K53!#3#
!/…rw{%&†ru‡xy€ˆ*M.D1Z1„+,1/
$DJ/%&'()*+,,-.!3!!"!/{'&%‰p'sw%uyŠ*M.D
1aa„1`M/
D/%&'()*+,,Z.#Y!!"GK!3#!#
!!"! !!!K#!6!/nop
nqrqstruv'&qwxy
z*1.DML`/
X]5DX/%&'()*+,,-.B!G!!!!/
{|w(%qw}wq~x%xyˆ€*NB.DN-L+„N-LL/
C!!D/%&'()*+,,1.!53!"!3"K"
!#3"!!/{'&‚%s%&y€‹*1.D+1„+`/
C!!DJ/%&'()*+,,E."33!!!!
!/nqrqstruv'&qwxy€€*1`.D++Z1„++Za/
4!DY/%&'()*+,,E.$"!"!G!0!!
4/{|w(%qw}wq~x%xyˆŠ*NB.DNML-„NMLa/
4!"DY/%&'()*+,,`.m!5!""!G!!"D!3!
!D!0!3 "#/‚%srv%nqr(y*+.D`/
YDX/%&'()*1ZZZ.YBJG3"!!!Œ!/{|w(%qw
}wq~x%xy€*1.D--„-`/
\DN/*+,,1.QI/nqr&%wŽ…rt&†'u%s&%us%&%‘ru&y€*M.D11a„1+,/
JD/%&'()*+,,-.X!!3!0#3
/{|w(%qw}wq~x%xyˆ€*NB.DN-Za/
!DQ/%&'()*+,,,.RB\GK00!##
!"!"3"!/{|w(%qw}wq~x%xy€‹*1`.DM--+„M---/
5DI/%&'()*+,,E.QRBNG"!#3!!/{|w(%qw
}wq~x%xyˆŠ*NB.DNLML/
S"!DQ/T4!6D4/*+,,-.I!"!!##!/{'&
o%~y
z*`.Da`Z„aZZ/
PDN/T"6D/*1ZZ`.I0#!3OKO!5/{'&|u%y
ˆˆ*EE`-.D--,„--+/
[!DB/%&'()*+,,,.NBJG3!!"!/{|w(%qw}wq~x%xy
€‹*1.D+`Z„+Z1/