SUMO1/sen in/SMT3 speci ic pep idase 2
(SENP2/AXAM2) : Time beha iou al s udy o 3 d o de
combina ions in WNT3A s imula ed HEK 293 cells
sh ip akash sinha
Independen Resea che ; O cid ID : o cid.o g/0000-0001-7027-5788
Add ess : 104-Madhu isha Heigh s Phase 1, Risali, Bhilai-490006, India
Co esponding au ho email : sinha.sh ip [email protected]
Abs ac
SENP2 is cys eine p o ease ha belongs o he amily o sen in-speci ic p o ease,
which come unde he b oade g oup o SUMO-speci ic isopep idases and p o eases.
The ubiqui in-like SUMO (small ubiqui in- ela ed modi ie ) sys em is a pos - ansla ional
p o ein modi ica ion pa hway in euka yo es, whe e SUMOyla ion is a highly dynamic
p ocess and deconjuga ion (deSUMOyla ion) is ca alyzed by a amily o cys eine p o-
eases, e med SUMO-speci ic p o eases o SUMO isopep idases. SENP2 p ocesses
newly syn hesized SUMO1 in o he conjuga able o m and ca alyze he deconjuga ion
o SUMO1-con aining species. Guj al and MacBea h [1] p o ides a quan i a i e, and
dynamic s udy o WNT3A-media ed s imula ion o HEK 293 cells, whe e hey eco d
ime based exp ession p o iles o se e al esponse genes which co ela ed signi ican ly
wi h p oli e a ion and mig a ion. By moni o ing he dynamics o gene exp ession us-
ing sel -o ganizing maps, hey iden i ied clus e s o genes ha exhibi simila exp es-
sion dynamics and unco e ed p e iously un ecognized posi i e and nega i e eedback
loops. Howe e , hei s udy depic s/uses singula measu emen s o indi idual gene
exp ession a di e en ime snapsho s/poin s o in e he sys em wide analysis o he
pa hway. A any pa icula ime poin , i is o en he case ha genes a e wo king syne -
gis ically in combina ions, e en hough hei exp ession measu emen s a e singula in
na u e. He e, I •enume a e and ank all 2415 SENP2 ela ed 3 d o de combina ions in
a o es o 71C3combina ions using ou di e en sensi i i y me hods; •show he con-
se ed ankings o SENP2-X-X combina ions, which poin o exis ence o biological
syne gy o some o hese combina ions ac oss he di e en sensi i i y me hods; and •
s udy he beha iou o some o hese combina ions ela ed o WNT3A esponse genes
ha a e anked by he machine lea ning sea ch engine (Sinha [2]) in ime. Pa e ns o
combina ions eme ge, some o which ha e been es ed in we lab, while o he s equi e
u he we lab analysis.
ITime beha iou al s udy o 3-od SENP2 comb. in WNT3A s imula ed cells
1Aspec s o unpublished wo k we e p esen ed in a pos e session a Cell Symposia: Technology. Biology.
Da a Science, 9-11 Oc obe 2016, Be keley, Cali o nia, USA.
P ep in submi ed o P ep in Ma ch 10, 2025
Keywo ds: Sensi i i y analysis, Suppo ec o anking, Hilbe Schmid
Independence C i e ion indices (HSIC) and Sobol indicies, WNT3A
1. Signi icance
Sinha [2] ecen ly demons a ed he use o machine lea ning based sea ch engine o
ank/ e eal gene combina ions a 2nd o de o he ime se ies da a by Guj al and
MacBea h [1] and showed how i is possible o loca e combina ions o p io i y ha
migh be wo king syne gis ically, using sensi i i y me hods and powe ul suppo ec-
o anking algo i hm. Howe e , he p oblem explodes combina o ially wi h e en a
small se o 71 eco ded genes in he s udy by Guj al and MacBea h [1], when one
s eps o explo e 3 d o de combina ions. Wi h he o al numbe o 71C3(= 57155) com-
bina ions, i becomes nea ly impossible o any biologis o s udy he sys em wide dy-
namics o any pa hway. Also, he amoun o ime usually needed o sea ch o and es
a combina ion is a mo e han he sea ch down by he machine lea ning based sea ch
engine. He e, I ex end he esea ch wo k by Sinha [2] o conduc a beha io al s udy o
3 d o de SENP2 ela ed combina ions using indi idual gene exp essions measu ed in
ime, in WNT3A s imula ed HEK 293 cells.
2. In oduc ion
The de ails o he machine lea ning based sea ch engine has been ecen ly published in
Sinha [2] and deployed o explo e he 2nd o de combina ions o genes in he da a se
p o ided by Guj al and MacBea h [1]. Ne e heless, he e, I poin o he undamen als
o he published wo k o comple eness.
2.1. A combina o ial p oblem
Sensi i i y analysis plays a majo ole in compu ing he s eng h o he in luence o
in ol ed ac o s in any phenomena unde in es iga ion. When applied o exp ession
p o iles o a ious in a/ex acellula ac o s ha o m an in eg al pa o a signaling
pa hway, he a iance and densi y based analysis yields a ange o sensi i i y indices
o indi idual as well as a ious combina ions o ac o s. These combina ions deno e
he highe o de in e ac ions among he in ol ed ac o s. Compu a ion o highe o -
de in e ac ions is o en ime consuming bu i gi es a chance o explo e he a ious
combina ions ha migh be o in e es in he wo king mechanism o he pa hway. Fo
example, in a ange o ou h o de combina ions among he a ious ac o s o he Wn
pa hway, i would be easy o assess he in luence o he des uc ion complex o med by
APC, AXIN, CSKI and GSK3 in e ac ion. Bu he e ec o hese combina ions a y
o e ime as measu emen s o old changes and de ia ions in old changes a y. So
i is impe a i e o know how an in e ac ion o a combina ion o he in ol ed ac o s
beha e in ime and Sinha [2] de elops a p ocedu e o ack he beha iou by exploi ing
he in luences o hese in ol ed ac o s.
2
2.2. A possible solu ion
In his wo k, a e es ima ing he indi idual e ec s o ac o s o a highe o de combi-
na ion, he indi idual indices a e conside ed as disc imina i e ea u es. A combina ion,
hen, is a ea u e se in highe o de (≥2 ,i.e mul i a ia e). Wi h an excessi ely la ge
numbe o ac o s in ol ed in he pa hway, i is di icul o sea ch o impo an com-
bina ions in a wide sea ch space o e di e en o de s. Exploi ing he analogy wi h
he issues o p io i izing webpages using anking algo i hms, o a pa icula o de , a
ull se o combina ions o in e ac ions can hen be p io i ized based on hese ea u es
using a powe ul anking algo i hm ia suppo ec o s Joachims [3]. Reco ding he
changing ankings o he combina ions o e ime e eals how highe o de in e ac ions
beha e wi hin he pa hway and when an in e en ion migh be necessa y o in luence
he in e ac ion wi hin he pa hway.
2.3. SUMO1/sen in/SMT3 speci ic pep idase 2 (SENP2)
Pos ansla ional modi ica ion wi h small ubiqui in- ela ed modi ie (SUMO) p o eins
is a key egula o y p o ein modi ica ions in euka yo ic cells whe e, p o eins in ol ed
in p ocesses like ch oma in o ganiza ion, ansc ip ion, DNA epai , mac omolecu-
la assembly, p o ein homeos asis, a icking, and signal ansduc ion a e subjec o
e e sible sumoyla ion. Flo ho and Melchio [4] summa ize basic mechanisms and
highligh ecen de elopmen s in he physiology o sumoyla ion. Ga eau and Lima
[5] elucida e an unde s anding o SUMO egula o y mechanisms which migh lead
o imp o ed app oaches o analysing he unc ion o SUMO and subs a e conjuga-
ion in dis inc cellula pa hways. In a summa y on SENPs, Nayak and Mulle [6]
s a e ha he known SUMO-speci ic isopep idases and p o eases a e cys eine p o-
eases ha a e classi ied in o h ee dis inc amilies: • he Ulp/SENP (ubiqui in-like
p o ease/sen in-speci ic p o ease) amily, • he Desi (deSUMOyla ing isopep idase)
amily and •USPL1 (ubiqui in-speci ic pep idase-like p o ein 1).
B ie ly, Ga eau and Lima [5] elucida e he SUMO conjuga ion cycle in a ew s eps,
which i ei e a e o comple eness (Fo g aphical unde s anding please see igu e 1 in
Ga eau and Lima [5]). •SUMO unde goes p ocessing by Ulps and SENPs o i s ma u e
o m, hus e ealing a ca boxy- e minal Gly-Gly mo i . •SUMO is hen adenyla ed
by he SUMO-ac i a ing enzyme subuni 1 (SAE1)-ubiqui in-like ac i a ing enzyme
subuni 2 (UBA2) E1 complex in an ATP◦Mg2+-dependen eac ion and ans e ed o
he ca aly ic Cys o he UBA2 subuni ; •Following ac i a ion, SUMO is ans e ed o
he ca aly ic Cys o he E2 conjuga ing enzyme, ubiqui in-like conjuga ing enzyme 9
(UBC9). •I can hen ca alyze conjuga ion o a subs a e in an E3 ligase-independen
manne h ough ecogni ion o SUMO consensus mo i s (ΨKXE) ha con ain a Lys
accep o esidue. In addi ion, SUMO ligases can acili a e SUMO ans e h ough
dis inc mechanisms. The au ho s depic h ee di e en mechanism o his om s eps
5 o 7 in igu e 1 o Ga eau and Lima [5]. Subs a e speci ici y impa ed by E3-subs a e
in e ac ions a e hough o be pa icula ly impo an o di ec ing conjuga ion o non-
consensus Lys esidues. •Subs a es modi ied by SUMO can con ac SUMO-binding
p o eins h ough hei SUMO-in e ac ing mo i s (SIMs). Finally, •Deconjuga ion is
pe o med by Ulp and SENP p o eases and ee SUMO may be ecycled o ano he
3
ound o conjuga ion.
AXIN o ms a complex wi h adenoma ous polyposis coli (APC) gene p oduc ,
glycogen syn hase kinase-3b (GSK3β), β-ca enin, DVL, and p o ein phospha ase 2A
(PP2A) and unc ions as a sca old p o ein in he WNT signaling pa hway. In he AXIN
complex, GSK3βphospho yla es β-ca enin, which is hen ubiqui ina ed and deg aded
by p o easome. Kadoya e al. [7] isola ed a no el p o ein ha binds o AXIN and named
i AXAM ( o Axin associa ing molecule). AXAM o med a complex wi h AXIN in
in ac cells and bound di ec ly o AXIN, hus inhibi ing he complex o ma ion o DVL
wi h AXIN and he ac i i y o DVL o supp ess GSK3β-dependen phospho yla ion o
AXIN. Fu he mo e, hey obse ed ha AXAM induced he deg ada ion o β-ca enin
in SW480 cells and inhibi ed WNT-dependen axis duplica ion in Xenopus emb yos.
Thei esul s sugges ed ha AXAM egula es he WNT signaling pa hway nega i ely
by inhibi ing he binding o DVL o AXIN.
Nishida e al. [8] cloned and cha ac e ized SUMO-1/Sm 3-speci ic isopep idase,
SMT3IP2/AXAM2 (Sm 3-speci ic isopep idase 2). The sequence da a indica ed ha
he amino acid sequence o SMT3IP2 was mos ly iden ical o ha o a AXAM, which
binds o AXIN and p omo es he deg ada ion o β-ca enin. Based on his, he au ho s
designa ed his isopep idase SMT3IP2/AXAM2. Fu he , when human SW480 cells
we e ans ec ed wi h wild- ype SMT3IP2/AXAM2, β-ca enin disappea ed. Also, i
was obse ed ha when he cells we e ans ec ed wi h he SMT3IP2/AXAM2 C500A
mu an , which had nei he isopep idase no ca boxyl- e minal hyd olase ac i i y, o
wi h he 1-352 mu an , which lacked he ca aly ic domain o he enzyme, again β-
ca enin disappea ed, indica ing ha he enzyme ac i i ies we e no necessa y o he
ins abili y o β-ca enin in his ans ec ion assay sys em and ha i s compe i ion wi h
DVL o binding o AXIN may be impo an o he ins abili y o β-ca enin as sug-
ges ed p e iously o AXAM by Kadoya e al. [7].
AXAM induces he deg ada ion o β-ca enin in SW480 cells (human colon cance
cells) and inhibi s axis o ma ion in Xenopus emb yos. Kadoya e al. [9] show ha
AXAM has he ca aly ic ac i i y o emo e SUMO-1 om sumoyla ed p o eins and
ha i s mu an wi hou his ac i i y is less able o down egula e β-ca enin and o inhibi
axis o ma ion o Xenopus emb yos. Thei esul s demons a e ha AXAM unc ions
as a desumoyla ion enzyme o down egula e β-ca enin in mammalian cells and sugges
ha sumoyla ion is in ol ed in he egula ion o he WNT signaling pa hway.
I p esen 3 d o de combina ions o SENP2 wi h o he genes, ha he machine
lea ning based sea ch engine poin s o, as possible syne gis ic combina ions ha migh
be wo king in ime.
3. Me hods
Please e e o sec ions o Sinha [2] o me hods, design o s udy and analysis o da a
o 2nd o de combina ions. The same me hod and design o s udy is used o gene a e
esul s o 3 d o de combina ions p esen ed in his s udy.
4
4. Time se ies da a
Guj al and MacBea h [1] p esen a se o 71 WNT- ela ed gene exp ession alues o 6
di e en imes poin s o e a ange o 24-hou pe iod using qPCR. The changes ep e-
sen he old-change in he exp ession le els o genes in 200 ng/mL WNT3A-s imula ed
HEK 293 cells in ime ela i e o hei le els in uns imula ed, se um-s a ed cells a 0-
hou . Guj al and MacBea h [1] s a e ha qPCR da a a e he means o h ee biological
eplica es. Only genes whose mean ansc ip le els changed by mo e han wo- old a
one o mo e ime poin s du ing he 24-hou ime cou se we e conside ed signi ican .
Posi i e (nega i e) numbe s ep esen up (down) - egula ion. We ha e al eady co e ed
he issues ela ed o hese da a se s in de ail in Sinha [10]. Reade s a e eques ed o
go h ough hem in he poin ed e e ence. The ools o s udy which a e used he e ha e
been published in ano he ounda ional wo k in Sinha [10].
5. Design o expe imen
5.1. Pipeline o ime se ies da a
Fo he case o ime se ies da a, in e ac ions among he con ibu ing ac o s a e s udied
by compa ing iple s o old-changes a single ime poin s. The p odecu e begins wi h
he gene a ion o dis ibu ion a ound measu emen s a single ime poin s wi h added
noise is done o es ima e he indices. A dis ibu ion is gene a ed o he old changes
a single ime poin s. Then o e e y gene, he e is a ec o o alues ep esen ing old
changes as well as de ia ions in old changes o di e en ime poin s and du a ions
be ween ime poin s, espec i ely. Nex a lis ing o all Cn
kcombina ions o knumbe
o genes om a o al o ngenes is gene a ed. kis ≥2 and ≤(n−1). Each o he com-
bina ion o o de k ep esen s a unique se o in e ac ion be ween he in ol ed gene ic
ac o s. A e his, he da ase s a e combined in a speci ed o ma which go as inpu
as pe he equi emen o a pa icula sensi i i y analysis me hod. Thus o each p h
combina ion in Cn
kcombina ions, he da ase is p epa ed in he equi ed o ma om
he dis ibu ions o wo sepa a e cases which ha e been discussed abo e. (See .R code
in mainSc ip -1-1.R). A e he da a has been ans o med, ec o ized p og amming
is employed o densi y based sensi i i y analysis and looping is employed o a i-
ance based sensi i i y analysis o compu e he equi ed sensi i i y indices o each o
he pcombina ions. This p ocedu e is done o di e en kinds o sensi i i y analysis
me hods.
A e he abo e sensi i i y indices ha e been s o ed o each o he p h combina-
ion, he nex s ep in he design o expe imen is conduc ed. Since he e is only one
eco ding o sensi i i y index pe combina ion, each combina ion o ms a aining ex-
ample which is allo ed a aining index and he sensi i i y indices o he indi idual
gene ic ac o s o m he aining example. Thus he e a e Cn
k aining examples o k h
o de in e ac ion. Using his aining se SVMRank
lea n Joachims [3] is used o gene a e a
model on de aul alue C alue o 20. In he cu en expe imen on oy model C alue
has no been unned. The aining se helps in he gene a ion o he model as he di -
e en gene combina ions a e numbe ed in o de which a e used as ank indices. The
5
model is hen used o gene a e sco e on he obse a ions in he es ing se using he
SV MRank
classi y Joachims [3]. No e ha due o a ailabili y o only one example pe com-
bina ion, a e he model has been buil , he same aining da a is used as es da a o
gene a es he sco es. This p ocedu e is execu ed o each and e e y sensi i i y analysis
me hod. This is ollowed by so ing o hese sco es along wi h he ank indices (i.e he
aining indices) al eady assigned o he gene combina ions. The end esul is a so ed
o de o he gene combina ions based on he anking sco e lea ned by he SV MRank
algo i hm. Finally, his en i e p ocedu e is compu ed o sensi i i y indices gene a ed
o each and e e y old change a ime poin and de ia ions in old change a di e en
du a ions. Obse ing he changing ank o a pa icula combina ion a di e en imes
and di e en ime pe iods will e eal how a combina ion is beha ing.
No e ha he ollowing is he o de in which he iles should be execu ed in R, in
o de , o ob aining he desi ed esul s (No e ha he code will no be explained he e) - •
use sou ce(”mainSc ip -1-1.R”) wi h a gumen s o Dynamic da a •sou ce(”SVMRank-
Resul s-D.R”), o ank he in e ac ions (again his needs o be done sepa a ely o
di e en kinds o SA me hods), •use sou ce(”Combine-Time- iles.R”), i compu -
ing indices sepa a ely ia p e ious ile, •sou ce(”So -n-Plo -D.R”) o so he in e -
ac ions. No e ha he so ing is chages he in e ac ion anking in ime. Thus •use
sou ce(”In e ac ion-P io i y-In ime.R”) o ind he p io i ized anking o each and e -
e y in e ac ion o e he di e en ime poin s and inally •use sou ce(”P in -Ranking-
AND-In e ac ion-Rank.R”) o p in indi idual anking o he equi ed inpu ac o wi h
o he in e ac ion ac o s.
6. Resul s & Discussion
6.1. Time se ies da a by Guj al and MacBea h [1]
NOTE - Ranking was assigned on sco es ha we e so ed in DECREASING alues.
So, 1 was assigned o highes sco e and ice e sa.
Resul s o he 3 d o de in e ac ions a e p esen ed he e. The esul s i s discuss
he beha iou o in e ac ions ac oss he snapsho s o ime using he compu ed sensi-
i i ies on old change measu emen s pe ime snapsho . The analysis was done us-
ing 4 di e en sensi i i y indices. Ou o he 71C3combina ions, I conside /p esen
only hose combina ions ha show a anking wi hin i s 10,000 ou o 57,155. This
choice is libe al and biologis s/oncologis s can ha e a mo e s ic e choice as pe need.
Two obse a ions a e made, • he anking o a pa icula combina ion is conse ed (i.e
wi hin he 10,000 ange) in a pa icula ime poin o in he ea ly phase o la e phase
o WNT3A s imula ion, ac oss he majo i y o he ou sensi i i y me hods, which is a
s ic c i e ia o assessmen o • he anking o a pa icula combina ion is conse ed
ac oss ime poin s/phase (i.e hey a e wi hin he 10,000 ange) and he majo i y o he
ou sensi i i y me hods, which is elaxed c i e ia o assessmen . Applying his il e
helps e eal impo an combina ions o in e es ha migh be wo king syne gis ically
a a highe o de le el in he cell.
Rega ding echnical poin s o implemen a ion, he ankings we e gene a ed wi h-
ou scaling/no malizing he ime se ies da a p o ided by Guj al and MacBea h [1].
6
Fo es ima ing he sensi i i y indices, a small gaussian dis ibu ion using he unc ion
no m ha gene a es a ec o o no mally dis ibu ed andom a iables gi en a ec o
leng h n (he e 9, he 10 h one is he mean/ eco ded gene egula ion i sel ), a popula ion
mean µand popula ion s anda d de ia ion σ. The syn ax o using no m is as ollows:
no m(n, mean, sd). Fu he , I use he ji e un ion o add a li le bi o noise o he
da a. This helps o see i he gene a ed ankings a e obus o no .
6.2. Enume a ion and anking o 2415 SENP2-X-X combina ions
om Guj al and MacBea h [1]
In he supplemen a y sec ion, I p esen ou iles, each con aining he ankings o 3 d
o de combina ions, ha wa y in ime (shown o 5 ime poin s). Each ile ep esen s
he ankings compu ed using a pa icula sensi i i y me hod. The changing ankings
in ime o a pa icula combina ion ep esen s he impo ance o con ibu ion/ ole ha
combina ion plays in he cell s imula ed wi h WNT3A. The sensi i i y me hods used
a e Hilbe Schmid Independence C i e ion indices (HSIC) indices (wi h b and linea
ke nel in Da Veiga [11]) and Sobol indicies (wi h 2002 implemen a ion in Sal elli [12]
and ma inez implemen a ion in Ma inez [13] and Baudin e al. [14]).
6.3. Conse ed machine lea ning ankings o es ed SENP2-X-X
combina ions
A o al o 2415, 3 d o de combina ions in ol ing SENP2 we e ob ained om a ull se
o 71C3= 57155 combina ions. Fu he , om his selec ed se , using he abo e c i e ia
o conse ed ankings, I epo / abula e he meaning ul combina ions ha migh be
wo king syne gis ically. Tables 2, 3 and 4 show he ankings o he same combina-
ions as in able 1, bu using b ke nel o HSIC, 2002 implemen a ion o SOBOL
and ma inez implemen a ion o SOBOL, espec i ely. As one allies he ankings o
ac oss hese ables o a pa icula combina ion, one inds ha he ole o he combina-
ion o in e es is conse ed. This conse a ion poin s o he exis ence o he biological
syne gy, whe he he combina ion has been es ed o unexplo ed/un es ed.
6.3.1. Examining he beha iou o AXIN1-SENP2-X combina ions
In he abo e li e a u e e iew, i shown ha SENP2 binds wi h AXIN. Looking a he
ables abo e, one inds he ollowing combina ions o AXIN1 along wi h SENP2, o
be p ominen a 3 d o de le el - AXIN1-FZD2-SENP2 and AXIN1-MYC-SENP2. All
hese combina ions indica e he exis ence o a possible syne gy when hey ake a highe
ank in he lis o combina ions.
6.3.2. Examining he beha iou o DVL-SENP2-X combina ions
Fu he , due o he abo e binding o SENP2 wi h AXIN, SENP2 inhibi s he o ma ion
o complex o AXIN wi h DVL, which educes he unc ioning o he WNT pa hway.
This nega i e syne gy be ween SENP2 and DVL also gi es insigh as o which com-
bina ion o DVL-SENP2 is ge ing a ec ed a a pa icula ime. Looking a he ables
7
RANKING @ iUSING HSIC - LINEAR
3 d o de comb. 1 3 6 12 24 3 d o de comb. 1 3 6 12 24
FBXW11-LRP6-SENP2 1 34823 45217 17593 40419 DKK1-JUN-SENP2 3 13146 45291 34681 42815
CXXC4-PORCN-SENP2 10 33446 17033 17387 32253 CSNK1D-FGF4-SENP2 12 15434 36642 38886 8419
CSNK2A1-MYC-SENP2 13 32182 51840 11657 9637 FOSL1-FRAT1-SENP2 24 25444 38488 23401 24549
APC-FZD6-SENP2 26 11930 12152 51400 36485 APC-PITX2-SENP2 37 14630 40719 18877 15582
DVL2-JUN-SENP2 40 7571 46728 17699 4151 FZD1-NLK-SENP2 66 7254 6519 12561 16204
DKK1-DVL2-SENP2 73 6472 32886 33074 53536 CSNK1G1-NLK-SENP2 74 35675 3308 48520 19328
FZD7-NKD1-SENP2 78 10179 4761 28020 28474 CCND2-LRP6-SENP2 83 56244 18182 20944 394
CXXC4-FOSL1-SENP2 88 36639 18548 29008 12844 LRP5-NLK-SENP2 99 17426 20510 156 54321
FRZB-JUN-SENP2 109 12704 33983 8160 2937 DKK1-LRP6-SENP2 117 30001 55075 39664 8461
DIXDC1-NKD1-SENP2 139 26878 5252 13422 20937 CTBP2-CTNNB1-SENP2 141 36145 41533 3064 6745
DAAM1-LRP6-SENP2 142 53280 45015 4819 36940 FZD5-CCND2-SENP2 150 29656 19798 20159 54229
FSHB-FZD2-SENP2 155 15792 56338 24860 16086 FZD5-CCND3-SENP2 179 12580 12647 25661 981
FZD7-PORCN-SENP2 204 27924 5434 9587 14745 DKK1-PYGO1-SENP2 253 27760 37224 42160 22797
CSNK1D-PORCN-SENP2 254 26488 43944 21480 22511 FOSL1-PPP2R1A-SENP2 256 39545 1842 16944 18375
FRZB-MYC-SENP2 259 14872 1551 37339 16113 AES-EP300-SENP2 266 39979 55044 31248 12673
SENP2-FBXW4-WNT3A 274 39131 29 44525 46327 DKK1-MYC-SENP2 288 24145 39527 40800 42346
FBXW2-PYGO1-SENP2 295 47321 21813 9500 57018 FRAT1-NLK-SENP2 308 14795 5137 12639 16597
FRZB-GSK3A-SENP2 323 15116 1689 3761 6417 CXXC4-FGF4-SENP2 325 44612 33138 54156 47148
DKK1-FOSL1-SENP2 326 21740 41468 36036 47108 FZD5-PITX2-SENP2 328 35236 22541 1156 14803
DKK1-FOXN1-SENP2 342 12351 29242 3585 34803 FOSL1-PORCN-SENP2 349 31659 11861 10245 21849
FZD5-MYC-SENP2 356 21029 5031 27635 17098 FOSL1-NLK-SENP2 359 18070 3202 3757 21594
DAAM1-PYGO1-SENP2 365 46893 25207 11837 39100 FZD5-PORCN-SENP2 377 32693 14759 8273 55426
FZD1-PORCN-SENP2 382 25494 17903 13765 16485 FBXW11-FOXN1-SENP2 392 5743 6882 5378 5741
DKK1-PORCN-SENP2 400 29700 53693 2734 52517 FRZB-FZD2-SENP2 403 12012 17053 8131 21847
CSNK1G1-PORCN-SENP2 410 36322 35831 12245 17913 CSNK1G1-FZD2-SENP2 430 26396 20526 35632 16355
DKK1-PPP2R1A-SENP2 442 14095 52078 45675 54675 CTNNBIP1-JUN-SENP2 451 45193 55478 33408 6827
FOSL1-JUN-SENP2 458 25557 50663 10786 1378 APC-PORCN-SENP2 466 12387 7261 13497 19215
FRZB-PORCN-SENP2 467 13159 11733 10122 22264 GSK3B-LRP6-SENP2 469 39713 22216 39819 33008
DVL1-MYC-SENP2 471 36864 4815 28745 33686 FZD5-FOXN1-SENP2 473 7569 6670 5785 7868
LRP5-PORCN-SENP2 476 41616 8750 51278 21981 FZD6-PORCN-SENP2 497 45212 45263 687 14394
AES-FOXN1-SENP2 518 22315 8527 7631 2724 DIXDC1-PITX2-SENP2 526 28707 7274 5676 35235
FZD7-PPP2CA-SENP2 540 11483 354 3539 34512 BCL9-FGF4-SENP2 548 29256 46172 46692 39145
FRZB-LRP5-SENP2 559 19130 1798 1543 5708 CTBP2-FOXN1-SENP2 566 19815 6401 2342 17983
FZD5-GSK3A-SENP2 569 25593 683 21843 18713 FSHB-NKD1-SENP2 574 7025 14205 7566 35992
DKK1-NKD1-SENP2 575 5975 43246 35996 27099 FZD5-PYGO1-SENP2 593 19014 1524 25504 36744
SENP2-TLE1-TLE2 610 6333 16429 15833 19287 FBXW11-NKD1-SENP2 618 34583 6281 9193 28276
CSNK1D-FOXN1-SENP2 624 4830 5783 7469 36423 FZD8-PORCN-SENP2 639 19701 11231 9109 12830
FBXW11-GSK3B-SENP2 640 23534 27154 19849 22130 DKK1-FSHB-SENP2 641 24808 11118 11901 46995
DKK1-FRAT1-SENP2 669 29229 40235 2545 51616 SENP2-WNT1-WNT2B 701 40779 2190 9179 41846
FRZB-NKD1-SENP2 705 6025 7511 12942 30682 CSNK1G1-DVL2-SENP2 708 9805 19546 23999 8201
FBXW11-FGF4-SENP2 711 39559 55606 33012 11315 FRZB-LEF1-SENP2 746 18406 20494 19809 3129
NLK-PORCN-SENP2 751 51440 56864 21216 6122 FZD5-FZD2-SENP2 769 23664 3575 3654 30814
FZD1-FZD2-SENP2 791 9528 30021 12952 33087 SENP2-SFRP1-WNT2B 804 39477 39510 38291 12235
FOSL1-FOXN1-SENP2 808 25273 3965 4409 8541 FBXW11-RHOU-SENP2 810 39829 54582 1076 13192
CSNK1G1-LRP5-SENP2 821 46576 17464 17352 30361 CXXC4-JUN-SENP2 843 21048 50347 6595 9660
CSNK1G1-JUN-SENP2 855 23957 55112 11084 3256 FZD1-NKD1-SENP2 865 3117 15529 25963 26289
FRAT1-JUN-SENP2 876 27146 34459 14780 13983 SENP2-WNT1-WNT4 879 37625 2401 4412 29111
DVL1-FOXN1-SENP2 907 37314 6190 2465 34563 FRAT1-PORCN-SENP2 915 19198 9986 14436 18176
DVL1-FBXW11-SENP2 927 27739 8099 22915 52768 APC-FZD2-SENP2 934 24435 31374 10970 32370
FZD5-CTNNBIP1-SENP2 936 41581 21812 4533 34272 SENP2-FBXW4-WNT4 962 28442 9419 12651 42095
AXIN1-FZD2-SENP2 970 21704 36841 4481 4717 FRZB-FSHB-SENP2 1016 13136 7480 5202 23820
FRZB-LRP6-SENP2 1020 16728 2573 7208 6418 DKK1-LEF1-SENP2 1053 32782 23184 36091 24285
CSNK1G1-FSHB-SENP2 1054 47479 13640 1228 8996 KREMEN1-PORCN-SENP2 1055 20253 16697 487 37387
FZD7-GSK3A-SENP2 1057 22214 256 52631 33449 FSHB-GSK3A-SENP2 1073 16288 25162 18111 11005
FBXW11-JUN-SENP2 1078 21114 46139 41233 39344 EP300-GSK3B-SENP2 1093 42030 6696 7981 765
DIXDC1-LRP5-SENP2 1098 18807 1510 3942 4609 DAAM1-GSK3A-SENP2 1101 52332 26964 25607 49696
FZD1-GSK3A-SENP2 1104 10414 2123 23509 7420 DIXDC1-FZD2-SENP2 1148 28328 6949 7791 20834
AXIN1-MYC-SENP2 1162 8878 8434 19760 6540 CTBP1-GSK3A-SENP2 1213 25332 467 15589 11039
FBXW2-PORCN-SENP2 1224 33013 2285 41273 42593 FSHB-LEF1-SENP2 1229 12578 50301 24457 7777
GSK3B-RHOU-SENP2 1230 39467 21376 11806 9365 CSNK2A1-FOXN1-SENP2 1233 22059 16672 4525 3145
FBXW2-JUN-SENP2 1253 32758 51631 42897 55749 CSNK1G1-NKD1-SENP2 1257 16631 15972 26700 19860
BTRC-GSK3A-SENP2 1269 31571 50158 24473 28342 FRZB-PYGO1-SENP2 1288 22336 2406 8695 20479
FBXW11-FBXW2-SENP2 1293 31516 16133 5700 35658 FZD8-GSK3A-SENP2 1313 24932 915 45683 16569
Table 1: Rankings o SENP2-X-X. A lis o app oxima ely i s 125 combina ions wi h ankings below
10,000 ou o 57,155. SA - HSIC; Ke nel - linea
abo e, one inds he ollowing combina ions o membe s o he DVL amily along
wi h SENP2, o be p ominen a 3 d o de le el - DVL2-JUN-SENP2, DKK1-DVL2-
SENP2, DVL1-MYC-SENP2, DVL1-FOXN1-SENP2, DVL1-FBXW11-SENP2 and
8
RANKING @ iUSING HSIC - RBF
3 d o de comb. 1 3 6 12 24 3 d o de comb. 1 3 6 12 24
FBXW11-LRP6-SENP2 462 28989 38794 18690 24696 DKK1-JUN-SENP2 2445 33296 14766 10519 28087
CXXC4-PORCN-SENP2 9869 47028 41747 45009 41195 CSNK1D-FGF4-SENP2 2542 27165 19967 35638 32914
CSNK2A1-MYC-SENP2 698 26688 37719 17840 33212 FOSL1-FRAT1-SENP2 15910 20828 47008 39310 20122
APC-FZD6-SENP2 4000 27344 40691 10612 57100 APC-PITX2-SENP2 2251 31790 24604 4114 39754
DVL2-JUN-SENP2 4462 28972 39208 37581 33219 FZD1-NLK-SENP2 4216 33313 50995 20046 16713
DKK1-DVL2-SENP2 12170 26608 1445 16210 24013 CSNK1G1-NLK-SENP2 34480 34469 25805 4202 8014
FZD7-NKD1-SENP2 22248 3166 47262 13293 2567 CCND2-LRP6-SENP2 4694 56422 53343 22864 16505
CXXC4-FOSL1-SENP2 27232 42351 44650 16863 48178 LRP5-NLK-SENP2 28404 31921 48677 23545 26406
FRZB-JUN-SENP2 1481 18469 38799 27435 28090 DKK1-LRP6-SENP2 1861 37831 42104 4554 34077
DIXDC1-NKD1-SENP2 24325 22750 54264 38554 4248 CTBP2-CTNNB1-SENP2 20615 24125 47470 7727 18482
DAAM1-LRP6-SENP2 6978 55181 28837 993 26132 FZD5-CCND2-SENP2 1593 48667 56355 20858 31218
FSHB-FZD2-SENP2 722 17184 1804 8318 40473 FZD5-CCND3-SENP2 682 12899 44614 4156 28575
FZD7-PORCN-SENP2 12209 34605 55753 8086 12262 DKK1-PYGO1-SENP2 403 23098 9845 24707 36625
CSNK1D-PORCN-SENP2 5664 26748 24402 26200 37885 FOSL1-PPP2R1A-SENP2 36531 47500 56688 1297 8711
FRZB-MYC-SENP2 341 12601 46519 38771 50004 AES-EP300-SENP2 36742 43851 9360 56088 25857
SENP2-FBXW4-WNT3A 27065 27541 40533 55578 8502 DKK1-MYC-SENP2 954 23283 49758 23572 34187
FBXW2-PYGO1-SENP2 5592 54522 7624 18559 15058 FRAT1-NLK-SENP2 47712 35472 55874 27952 35046
FRZB-GSK3A-SENP2 1005 18367 54917 45435 43654 CXXC4-FGF4-SENP2 252 42683 39239 31323 30294
DKK1-FOSL1-SENP2 14095 26375 3333 23119 42212 FZD5-PITX2-SENP2 10435 42695 24116 3954 33353
DKK1-FOXN1-SENP2 1097 45908 33686 6660 22662 FOSL1-PORCN-SENP2 314 29835 38646 3075 34319
FZD5-MYC-SENP2 4758 9532 47106 17393 47394 FOSL1-NLK-SENP2 41514 24088 54636 21014 19349
DAAM1-PYGO1-SENP2 7009 46420 6762 21944 29682 FZD5-PORCN-SENP2 13359 46673 16639 12543 32648
FZD1-PORCN-SENP2 5513 34056 9744 10153 31014 FBXW11-FOXN1-SENP2 128 6559 40566 11817 4361
DKK1-PORCN-SENP2 2598 41263 6134 19723 13188 FRZB-FZD2-SENP2 2112 16652 26767 43657 55251
CSNK1G1-PORCN-SENP2 13585 41454 10606 1967 17443 CSNK1G1-FZD2-SENP2 16568 22383 10213 6975 36119
DKK1-PPP2R1A-SENP2 4320 17195 24869 14464 3866 CTNNBIP1-JUN-SENP2 42259 50095 40291 21021 34386
FOSL1-JUN-SENP2 15271 29847 41615 22047 48378 APC-PORCN-SENP2 311 33317 27533 12463 51663
FRZB-PORCN-SENP2 2427 25944 18926 35699 48606 GSK3B-LRP6-SENP2 2447 36212 52160 19143 45638
DVL1-MYC-SENP2 2855 32356 46420 20795 31751 FZD5-FOXN1-SENP2 755 12834 53767 11567 34539
LRP5-PORCN-SENP2 11545 45801 9754 1937 37320 FZD6-PORCN-SENP2 3 53444 8379 12707 32509
AES-FOXN1-SENP2 1218 24082 52757 25404 14040 DIXDC1-PITX2-SENP2 3537 43865 15972 13329 19669
FZD7-PPP2CA-SENP2 32571 2154 49346 21000 26293 BCL9-FGF4-SENP2 7646 28217 10273 19350 40259
FRZB-LRP5-SENP2 555 19606 45855 1859 48730 CTBP2-FOXN1-SENP2 7635 19129 49786 125 42056
FZD5-GSK3A-SENP2 1856 36876 56727 30350 43628 FSHB-NKD1-SENP2 14879 5325 16207 3306 6877
DKK1-NKD1-SENP2 7012 22034 30235 20793 14207 FZD5-PYGO1-SENP2 864 25856 32614 26549 46981
SENP2-TLE1-TLE2 22393 22753 3266 25737 12237 FBXW11-NKD1-SENP2 3968 23882 33729 15929 5877
CSNK1D-FOXN1-SENP2 1289 8520 39455 7070 25852 FZD8-PORCN-SENP2 1042 32328 3606 28410 19273
FBXW11-GSK3B-SENP2 5753 10714 20625 19385 4353 DKK1-FSHB-SENP2 13659 23744 54431 4021 33075
DKK1-FRAT1-SENP2 5714 28221 7591 6962 28179 SENP2-WNT1-WNT2B 2021 43379 30860 2867 24069
FRZB-NKD1-SENP2 3644 10458 50187 29431 36573 CSNK1G1-DVL2-SENP2 10060 33044 6346 24081 29517
FBXW11-FGF4-SENP2 460 23321 17102 23270 7399 FRZB-LEF1-SENP2 306 25220 39312 10442 24101
NLK-PORCN-SENP2 25839 52725 11882 9881 37272 FZD5-FZD2-SENP2 5895 34287 41654 30068 50389
FZD1-FZD2-SENP2 4443 13047 26746 40642 49778 SENP2-SFRP1-WNT2B 12477 36645 18903 52949 54446
FOSL1-FOXN1-SENP2 1644 24800 52856 5786 32696 FBXW11-RHOU-SENP2 2811 29045 28581 338 17622
CSNK1G1-LRP5-SENP2 14135 47074 22615 10563 18356 CXXC4-JUN-SENP2 1851 32478 55139 8858 43014
CSNK1G1-JUN-SENP2 2057 43819 27038 14070 17638 FZD1-NKD1-SENP2 16283 248 42563 17609 26499
FRAT1-JUN-SENP2 8350 32873 42151 5535 36295 SENP2-WNT1-WNT4 595 42309 31627 659 12885
DVL1-FOXN1-SENP2 3061 30960 37499 23295 15142 FRAT1-PORCN-SENP2 1688 40659 28876 5431 52097
DVL1-FBXW11-SENP2 10393 17940 54581 8945 22213 APC-FZD2-SENP2 324 36486 16060 22102 42466
FZD5-CTNNBIP1-SENP2 4249 39970 22055 26513 16307 SENP2-FBXW4-WNT4 7957 13325 39354 38785 4122
AXIN1-FZD2-SENP2 8182 15407 16562 39363 47191 FRZB-FSHB-SENP2 5870 14328 41622 369 53440
FRZB-LRP6-SENP2 1809 20940 39489 3847 40248 DKK1-LEF1-SENP2 1211 36246 13554 12065 5713
CSNK1G1-FSHB-SENP2 41253 35360 30966 2443 33408 KREMEN1-PORCN-SENP2 2897 40815 14540 5841 26554
FZD7-GSK3A-SENP2 290 25036 52263 13397 4756 FSHB-GSK3A-SENP2 6015 32214 13032 15982 30339
FBXW11-JUN-SENP2 2521 15541 36470 25945 625 EP300-GSK3B-SENP2 8327 37174 36829 10925 19701
DIXDC1-LRP5-SENP2 1777 23484 44827 123 12925 DAAM1-GSK3A-SENP2 1185 54603 39296 24751 14243
FZD1-GSK3A-SENP2 1003 14896 54197 10418 35326 DIXDC1-FZD2-SENP2 11918 40028 27691 41589 5926
AXIN1-MYC-SENP2 26539 8188 46118 33138 43486 CTBP1-GSK3A-SENP2 409 42665 56908 22557 34169
FBXW2-PORCN-SENP2 9048 55175 828 25406 16023 FSHB-LEF1-SENP2 16486 20092 5835 4015 10968
GSK3B-RHOU-SENP2 5807 32711 51623 1013 46591 CSNK2A1-FOXN1-SENP2 142 13206 48212 17145 40808
FBXW2-JUN-SENP2 25289 51870 3972 20307 1098 CSNK1G1-NKD1-SENP2 4079 7354 54740 12528 13804
BTRC-GSK3A-SENP2 9345 20665 52714 11947 10821 FRZB-PYGO1-SENP2 334 16496 42795 31671 51686
FBXW11-FBXW2-SENP2 5640 29344 45548 27448 44741 FZD8-GSK3A-SENP2 422 12723 55867 1253 13272
Table 2: Rankings o SENP2-X-X. A lis o app oxima ely i s 125 combina ions wi h ankings below
10,000 ou o 57,155. SA - HSIC; Ke nel - b
CSNK1G1-DVL2-SENP2. All hese combina ions indica e he exis ence o a possible
syne gy when hey ake a highe ank in he lis o combina ions.
9
