E1A binding p o ein p300 / his one ace yl ans e ase p300
(EP300) : 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
His one ace yl ans e ase p300 (p300 HAT) o adeno i us ea ly egion 1A(E1A)-associa ed
p o ein p300 (EP300) gene encodes he adeno i us E1A-associa ed cellula p300 an-
sc ip ional co-ac i a o p o ein. I unc ions as his one ace yl ans e ase ha egula es
ansc ip ion o genes ia ch oma in emodeling by allowing his one p o eins o w ap
DNA less igh ly. 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 ex-
p 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 using sel -
o ganizing maps, hey iden i ied clus e s o genes ha exhibi simila exp ession dy-
namics 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 EP300 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 conse ed ank-
ings o EP300-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.
Keywo ds: Sensi i i y analysis, Suppo ec o anking, Hilbe Schmid
Independence C i e ion indices (HSIC) and Sobol indicies, WNT3A
ITime beha iou al s udy o 3-od EP300 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1Aspec s o unpublished wo k we e p esen ed in a pos e session a Cell Symposia: Technology.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 4, 2025
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 EP300 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. E1A binding p o ein p300 / his one ace yl ans e ase p300 (EP300)
The g ow h-con olling unc ions o he adeno i us E1A oncop o ein depend on i s
abili y o in e ac wi h a se o cellula p o eins. Among hese a e he e inoblas oma
p o ein, p107, p130, and p300. Eckne e al. [4] isola ed a cDNA encoding ull-leng h
human p300 and mapped he ch omosomal loca ion o he gene on he long (q) a m
o he human ch omosome 22 a posi ion 13.2. They show ha p300 con ains h ee
cys eine- and his idine- ich egions o which he mos ca boxy- e minal egion in e ac s
speci ically wi h E1A. In i s cen e , i con ains a b omodomain which is a hallma k o
ce ain ansc ip ional coac i a o s.
B omodomain was iden i ied as a no el s uc u al mo i when Tamkun e al. [5]
showed ha he b ahma (BRM) gene is equi ed o he ac i a ion o mul iple homeo ic
genes in D osophila. BRM encodes a 1638 esidue p o ein ha is simila o SNF2SWI2,
a p o ein in ol ed in ansc ip ional ac i a ion in yeas , sugges ing possible models o
he ole o BRM in he ansc ip ional ac i a ion o homeo ic genes. In addi ion, bo h
BRM and SNF2 con ain a 77 amino acid mo i ha is ound in o he D osophila, yeas ,
and human egula o y p o eins and may be cha ac e is ic o a new amily o egula o y
p o eins.
Og yzko e al. [6] demons a e ha p300/CBP is no only a ansc ip ional adap o
bu also a his one ace yl ans e ase. Is a ansc ip ional adap o ha in eg a es signals
om many sequence-speci ic ac i a o s ia di ec in e ac ions. The cellula p300/CBP
associa ed ac o (PCAF) possesses in insic his one ace yl ans e ase ac i i y, ha a -
ge s p300/CBP o modula e ansc ip ion and/o cell cycle p og ession. p300/CNP
ace yla es all ou co e his ones in nucleosomes and Va ious cellula and i al ac o s.
His one ace yla ion helps in ch oma in emodelling and gene ac i a ion. Nea ly all
known his one-ace yl ans e ase (HAT)-associa ed ansc ip ional co-ac i a o s con ain
b omodomains (app oxima ely 110-amino-acid modules ound in many ch oma in-
associa ed p o eins). Dhalluin e al. [7] epo ed he solu ion s uc u e o he b omod-
omain o he HAT co-ac i a o P/CAF (p300/CBP-associa ed ac o ) which e ealed an
unusual le -handed up-and-down ou -helix bundle. The na u e o he ecogni ion o
ace yl-lysine by he P/CAF b omodomain is simila o ha o ace yl-CoA by his one
ace yl ans e ase. Thus, he b omodomain is unc ionally linked o he HAT ac i i y o
3
co-ac i a o s in he egula ion o gene ansc ip ion.
Owen e al. [8] epo he c ys al s uc u e a 1.9 ˚
A esolu ion o he Saccha omyces
ce e isiae GCN5P b omodomain complexed wi h a pep ide co esponding o esidues
1529 o his one H4 ace yla ed a he ζ-N o lysine 16. They show ha his b omod-
omain p e e en ially binds o pep ides con aining an N-ace yl lysine esidue. Only
esidues 1619 o he ace yla ed pep ide in e ac wi h he b omodomain. Zeng and
Zhou [9] summa ize he b omodomains an an ace yl-lysine binding domain. The 61
b omodomains (BRDs) in he human genome clus e in o eigh amilies based on s uc-
u e/sequence simila i y. Filippakopoulos e al. [10] p esen 29 high- esolu ion c ys al
s uc u es, co e ing all BRD amilies.
I p esen 3 d o de combina ions o EP300 wi h o he genes, ha he machine lea n-
ing 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. 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 [11]. 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 [11].
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
4
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
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.
5
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].
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 EP300-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 [12]) and Sobol indicies (wi h 2002 implemen a ion in Sal elli [13]
and ma inez implemen a ion in Ma inez [14] and Baudin e al. [15]).
6.3. Conse ed machine lea ning ankings o es ed EP300-X-X com-
bina ions
A o al o 2415, 3 d o de combina ions in ol ing EP300 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
6
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 TCF-EP300-X combina ions
Sun e al. [16] epo ha he ansc ip ional coac i a o p300 in e ac s wi h β-ca enin
in i o and in i o and is c i ical o β-ca enin-media ed neoplas ic ans o ma ion. I
was ound o ac i a e β-ca enin/TCF ansc ip ion, and hei biochemical associa ion
equi es he CH1 domain o p300 and a egion o β-ca enin ha includes i s NH2-
e minal ansac i a ion domain and he i s wo a madillo epea s. Looking a he
ables abo e, one inds he ollowing combina ions o membe s o TCF amily along
wi h EP300, o be p ominen a 3 d o de le el - AES-EP300-TCF7, AXIN1-EP300-
TCF7, DVL1-EP300-TCF7, AES-EP300-TCF7L1, DVL1-EP300-TCF7L1, EP300-GSK3B-
TCF7, EP300-LRP6-TCF7, EP300-FOXN1-TCF7L1, EP300-FZD2-TCF7L1 and EP300-
PORCN-TCF7L1. 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 LEF1-EP300-X combina ions
To es whe he downs eam componen s o he WNT/β-ca enin signal ansduc ion
pa hway con ibu e o he di e en ial egula ion o Wn a ge genes, Hech and S emm-
le [17] asked whe he LEF1 and TCF4E we e equally capable o suppo ing ac i a ion
o WNT- egula ed p omo e s by β-ca enin and p300. A he Siamois p omo e and in
conjunc ion wi h LEF1, ec ui men and ac i a ion o p300 by β-ca enin appea s o be
su icien . Also, hei p elimina y esul s indica ed ha TCF1E, bu no TCF1B, which
esembles LEF1, could coope a e wi h β-ca enin and p300 o ac i a e he CDX1 p o-
mo e . Looking a he ables abo e, one inds he ollowing combina ions o LEF1
along wi h EP300, o be p ominen a 3 d o de le el - EP300-FZD2-LEF1. 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.
6.3.3. Examining he beha iou o CCND-EP300-X combina ions
Hech e al. [18] show ha β-ca enin and p300 syne gize o s imula e a syn he ic e-
po e gene cons uc , whe eas ac i a ion o he CCND1 p omo e by β-ca enin is e-
ac o y o p300 s imula ion. Looking a he ables abo e, one inds he ollowing
combina ions o membe s o CCND amily along wi h EP300, o be p ominen a
3 d o de le el - FZD5-CCND2-EP300, FZD5-CCND1-EP300 and CCND1-CTBP1-
EP300. 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.
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
DVL1-EP300-LRP5 45 28131 44550 28209 50928 AES-EP300-FRZB 107 47237 52432 18109 22006
DVL1-EP300-FRZB 116 18151 11685 9254 40545 AXIN1-EP300-GSK3B 163 24228 14803 32053 17651
DVL1-EP300-GSK3B 207 32638 7688 33872 35334 DVL1-EP300-WNT2B 247 6893 42213 52392 47037
AES-EP300-TCF7 257 52340 43783 40882 1516 AES-EP300-FZD1 258 49278 55037 15347 47022
AES-EP300-SENP2 266 39979 55044 31248 12673 DVL1-EP300-WNT4 272 18110 37869 41167 44769
DVL1-EP300-FBXW11 404 20946 9783 53163 54751 DVL1-EP300-FZD1 420 47837 24856 16322 41749
AXIN1-EP300-TCF7 421 7016 43416 54620 14023 EP300-JUN-KREMEN1 445 18545 22047 46724 18178
EP300-FBXW11-LRP6 502 27632 22035 22910 27044 EP300-LRP6-WNT2 638 44313 22577 3663 7256
EP300-GSK3B-RHOU 762 29861 9716 10624 2207 DVL1-EP300-SFRP4 803 36937 10257 53811 47697
AES-EP300-FBXW2 878 39324 31038 27397 3825 EP300-WNT1-WNT2 884 39083 11026 13187 5410
EP300-WNT1-WNT2B 940 30973 2609 12191 47783 EP300-GSK3B-TCF7 954 29218 27018 16078 23635
AXIN1-DVL1-EP300 1031 6065 16319 47978 31309 AXIN1-EP300-LRP5 1069 2036 46947 24321 4379
DKK1-EP300-FRZB 1088 10676 53202 44534 37008 EP300-GSK3B-SENP2 1093 42030 6696 7981 765
FZD5-CCND2-EP300 1109 33708 3119 30209 55972 EP300-RHOU-WNT2 1132 42400 48712 18390 28303
DVL1-EP300-TCF7 1158 46231 45665 56151 39460 AES-EP300-WNT5A 1232 50236 54302 23216 39305
EP300-FZD2-FZD7 1306 49961 52239 51266 19772 AXIN1-EP300-RHOU 1312 1646 32903 47413 5408
EP300-FOXN1-TLE2 1334 6564 2241 419 8940 EP300-LRP6-TCF7 1342 30447 49509 44129 4032
EP300-WNT1-WNT3A 1360 30527 695 53063 7375 EP300-FZD2-SFRP4 1428 43571 54834 3371 29414
EP300-LRP6-RHOU 1441 36401 11469 47312 1505 DVL1-EP300-SLC9A3R1 1490 18769 9009 57150 34851
AES-EP300-FOSL1 1521 46072 48935 20712 49058 EP300-FGF4-FRAT1 1588 28152 39282 54116 41791
EP300-FOXN1-SFRP4 1612 6840 5991 389 280 EP300-FOXN1-KREMEN1 1620 7884 6802 739 13419
AES-EP300-TCF7L1 1631 44460 34641 28386 39724 EP300-FZD2-SENP2 1639 43293 36216 3329 8258
EP300-FGF4-FOSL1 1656 55025 38932 40354 51107 EP300-WNT1-WNT5A 1667 20162 16144 44114 26527
AES-EP300-TLE2 1736 45932 19846 34789 55409 EP300-GSK3B-SFRP4 1785 42024 20409 8178 12158
EP300-FOXN1-FRAT1 1814 1637 5045 2015 815 AXIN1-EP300-SLC9A3R1 2064 7574 22759 53828 11686
EP300-GSK3B-WNT2B 2076 31297 1204 24013 16338 EP300-FGF4-WNT2 2093 38634 33059 42983 46200
AES-EP300-PITX2 2125 50901 43504 52709 17083 AXIN1-EP300-FBXW4 2130 13751 7349 18366 36793
EP300-LRP6-SLC9A3R1 2241 54665 6734 14185 31200 EP300-GSK3B-WNT2 2254 34471 22817 3013 1572
EP300-GSK3A-SENP2 2275 42378 2094 22319 42143 DVL1-EP300-FBXW4 2314 4738 8056 35532 41452
EP300-FZD2-WNT2B 2320 24458 22441 44903 18140 EP300-FBXW11-WNT2 2352 32380 5400 26107 31089
EP300-GSK3A-WNT2 2458 45111 24489 42270 47520 AES-EP300-NLK 2549 52374 48380 27425 55437
AXIN1-EP300-FRZB 2553 866 20410 2676 6170 EP300-PORCN-SENP2 2667 50915 5651 10035 52083
EP300-JUN-TLE2 2679 44828 31 25970 46852 EP300-FZD2-PPP2CA 2702 12448 13262 50046 20911
AES-EP300-FZD8 2713 38543 49818 22196 49165 EP300-FOXN1-FZD7 2714 25117 4781 3184 35097
EP300-GSK3B-SLC9A3R1 2733 48653 10966 10820 22885 EP300-PYGO1-WNT2 2948 43158 15314 8724 20816
DVL1-EP300-FZD8 2951 29540 12120 18903 44386 DVL1-EP300-WNT5A 2981 45215 32109 50904 36947
EP300-FZD2-LRP5 3002 41575 22148 54563 13500 EP300-PORCN-WNT4 3047 52212 12666 11882 56673
EP300-FOXN1-PPP2R1A 3054 31254 9485 1045 4738 AXIN1-EP300-SENP2 3106 10788 31481 23191 4091
EP300-FOXN1-FZD1 3113 1863 8770 1719 923 EP300-FOXN1-TCF7L1 3126 3782 3353 1217 4819
EP300-FZD2-WNT2 3139 39887 31858 26340 25585 EP300-JUN-WIF1 3213 26743 1259 1082 53260
AES-EP300-PPP2CA 3218 22740 43678 26060 41565 EP300-PORCN-SFRP1 3229 50142 13492 14922 54985
EP300-LRP6-FBXW4 3274 44837 28655 8993 14599 DKK1-EP300-LRP5 3312 11909 56702 45179 37104
EP300-SLC9A3R1-WNT2 3350 46806 34723 47893 8400 CCND1-CTBP1-EP300 3358 42042 42344 35857 48984
CTBP2-CTNNB1-EP300 3365 40136 27775 17397 7468 DVL1-EP300-KREMEN1 3366 29392 28100 54892 20990
EP300-PORCN-SFRP4 3399 53557 14432 13953 55277 DIXDC1-EP300-FBXW11 3401 6056 10476 24069 55750
EP300-FOXN1-FZD6 3411 4860 17749 501 25541 EP300-FRZB-FZD1 3480 44015 31205 1022 5684
EP300-FOXN1-LRP5 3486 2188 7346 15917 9396 AXIN1-EP300-FZD1 3503 369 27768 3828 12795
EP300-PORCN-PPP2R1A 3588 55435 38638 36180 44771 EP300-FZD2-WNT4 3653 44086 18558 21712 24613
AXIN1-EP300-WNT3A 3721 4489 13963 10072 11451 EP300-FZD2-TCF7L1 3731 10207 47941 32679 8909
AES-EP300-WNT2 3733 42752 47227 32967 26785 EP300-FZD2-PITX2 3771 12315 30396 16799 22718
DVL1-EP300-TCF7L1 3789 46595 17797 39924 51184 AES-EP300-KREMEN1 3796 45394 51834 52960 6499
EP300-FZD2-LEF1 3817 40487 19516 56270 7480 EP300-PORCN-WNT2B 3826 37202 48507 42391 54306
AXIN1-EP300-LRP6 3878 5642 33651 11423 13761 DVL1-EP300-PITX2 3886 37126 11319 53194 36735
DKK1-EP300-SENP2 3891 20732 50914 37657 44749 EP300-GSK3A-NLK 3902 24187 13268 22163 37611
EP300-FBXW11-SENP2 3933 42083 2536 20991 19946 EP300-FOXN1-WNT2B 3966 8828 3051 1383 6560
EP300-FBXW11-FBXW4 4014 31495 811 16846 39181 EP300-FGF4-PPP2R1A 4059 54172 38740 54434 30530
FZD5-CCND1-EP300 4060 18083 4714 3951 48122 EP300-JUN-PPP2R1A 4089 45635 48485 28347 10942
EP300-FOXN1-RHOU 4098 4360 4723 4476 13723 EP300-FOXN1-WNT4 4156 11103 5561 886 8761
EP300-GSK3B-LRP5 4172 45460 31410 26873 1387 AXIN1-EP300-WNT5A 4180 9970 29920 45061 25015
EP300-NKD1-WNT2 4238 5464 3982 38439 1323 AXIN1-EP300-WNT4 4260 2683 36665 20580 7537
EP300-GSK3B-FBXW4 4291 44257 21194 7041 8080 AXIN1-EP300-PITX2 4304 11293 12887 53659 13073
EP300-FOXN1-GSK3B 4325 2497 2297 15564 19880 EP300-PORCN-TCF7L1 4329 18128 11086 13559 52464
EP300-LRP6-SFRP4 4353 54017 12211 6672 17900 EP300-GSK3A-WNT2B 4370 31237 5657 53835 53021
Table 1: Rankings o EP300-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
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
DVL1-EP300-LRP5 52736 14122 3935 57133 11155 AES-EP300-FRZB 40882 51536 7119 33764 20536
DVL1-EP300-FRZB 50198 6937 30267 52396 2625 AXIN1-EP300-GSK3B 35345 3731 2610 56872 11778
DVL1-EP300-GSK3B 53115 9324 29348 56804 16941 DVL1-EP300-WNT2B 53233 2104 15799 56735 2280
AES-EP300-TCF7 39855 49176 5264 28073 35221 AES-EP300-FZD1 38410 50414 31342 5312 36922
AES-EP300-SENP2 36742 43851 9360 56088 25857 DVL1-EP300-WNT4 44214 8987 34040 43683 919
DVL1-EP300-FBXW11 52680 9754 26824 56227 7252 DVL1-EP300-FZD1 40171 42833 3293 53576 7127
AXIN1-EP300-TCF7 23920 5040 28002 41498 26154 EP300-JUN-KREMEN1 4639 142 27356 54948 19911
EP300-FBXW11-LRP6 51387 7749 39604 26908 55449 EP300-LRP6-WNT2 4956 43850 46302 4230 21219
EP300-GSK3B-RHOU 18018 15875 23808 17448 24731 DVL1-EP300-SFRP4 20719 16744 18619 55573 10227
AES-EP300-FBXW2 37663 38475 8684 26951 43448 EP300-WNT1-WNT2 1580 44154 51942 5979 10465
EP300-WNT1-WNT2B 2458 13992 29930 2629 26795 EP300-GSK3B-TCF7 10805 6455 14967 4039 31117
AXIN1-DVL1-EP300 3584 5186 25284 4738 39794 AXIN1-EP300-LRP5 46163 2225 27682 55146 32996
DKK1-EP300-FRZB 6801 5011 12885 30599 43081 EP300-GSK3B-SENP2 8327 37174 36829 10925 19701
FZD5-CCND2-EP300 2650 37698 56502 40799 52677 EP300-RHOU-WNT2 9914 43007 45594 678 52515
DVL1-EP300-TCF7 50918 34541 3163 55278 13295 AES-EP300-WNT5A 40140 51612 23938 4009 35408
EP300-FZD2-FZD7 16954 49764 37714 257 32349 AXIN1-EP300-RHOU 31074 6355 22262 56648 46901
EP300-FOXN1-TLE2 1483 17209 53526 19752 11793 EP300-LRP6-TCF7 2128 9836 35075 32339 23660
EP300-WNT1-WNT3A 1327 24404 26980 31626 25194 EP300-FZD2-SFRP4 2005 26142 28568 1038 19151
EP300-LRP6-RHOU 2252 29244 36048 53718 12738 DVL1-EP300-SLC9A3R1 53857 20248 11438 50841 13844
AES-EP300-FOSL1 43507 49548 17732 5048 38399 EP300-FGF4-FRAT1 2201 12179 25784 4990 46565
EP300-FOXN1-SFRP4 1251 4474 55453 13622 8030 EP300-FOXN1-KREMEN1 2486 110 54841 38583 4454
AES-EP300-TCF7L1 40724 47358 6323 29692 43075 EP300-FZD2-SENP2 4197 39519 18150 40601 47963
EP300-FGF4-FOSL1 4014 52588 15864 2361 53651 EP300-WNT1-WNT5A 2374 24154 16830 20295 34795
AES-EP300-TLE2 39879 47530 4903 40946 36137 EP300-GSK3B-SFRP4 8611 32039 42196 33914 2265
EP300-FOXN1-FRAT1 1892 1651 56769 4475 20697 AXIN1-EP300-SLC9A3R1 55614 15848 7372 37686 44246
EP300-GSK3B-WNT2B 17031 3072 9839 9763 7695 EP300-FGF4-WNT2 4612 34033 39415 40763 15139
AES-EP300-PITX2 46927 53837 1549 50756 32506 AXIN1-EP300-FBXW4 39191 32647 632 24287 49848
EP300-LRP6-SLC9A3R1 14878 54303 41153 14723 43225 EP300-GSK3B-WNT2 39218 19231 50369 11449 1474
EP300-GSK3A-SENP2 699 37681 53286 49758 22127 DVL1-EP300-FBXW4 42764 5391 2864 37529 23352
EP300-FZD2-WNT2B 10327 30918 21265 5368 12988 EP300-FBXW11-WNT2 28485 14388 54560 3248 12860
EP300-GSK3A-WNT2 11607 41760 54123 6698 20631 AES-EP300-NLK 38886 52106 1233 23736 42435
AXIN1-EP300-FRZB 24331 5929 26268 54326 22003 EP300-PORCN-SENP2 6992 46691 29845 18550 22225
EP300-JUN-TLE2 7910 43504 27573 32054 25082 EP300-FZD2-PPP2CA 8059 21295 864 5359 44323
AES-EP300-FZD8 42215 43804 6126 33921 25164 EP300-FOXN1-FZD7 3215 8590 56511 7008 39469
EP300-GSK3B-SLC9A3R1 36320 50164 49824 9817 11726 EP300-PYGO1-WNT2 5709 43420 44821 441 34191
DVL1-EP300-FZD8 47942 8331 10133 56556 21119 DVL1-EP300-WNT5A 45556 27855 659 56344 29253
EP300-FZD2-LRP5 36812 15690 6117 6565 23126 EP300-PORCN-WNT4 5823 49192 43675 49247 45902
EP300-FOXN1-PPP2R1A 1354 35385 45759 2306 27930 AXIN1-EP300-SENP2 19823 15581 10252 51019 28168
EP300-FOXN1-FZD1 800 1001 54131 249 2703 EP300-FOXN1-TCF7L1 1435 5591 57140 32094 6830
EP300-FZD2-WNT2 16652 30806 29163 34567 17667 EP300-JUN-WIF1 11523 21819 31185 9903 31253
AES-EP300-PPP2CA 40675 14926 3496 32198 22117 EP300-PORCN-SFRP1 25523 50771 36657 24398 41003
EP300-LRP6-FBXW4 2183 36856 32532 30812 36337 DKK1-EP300-LRP5 52435 1604 7145 16640 29132
EP300-SLC9A3R1-WNT2 12103 46092 24912 6681 4849 CCND1-CTBP1-EP300 31521 40575 10441 16973 2244
CTBP2-CTNNB1-EP300 30000 37842 42325 7348 17273 DVL1-EP300-KREMEN1 54034 12200 13668 57031 15029
EP300-PORCN-SFRP4 1223 52664 18944 37247 43717 DIXDC1-EP300-FBXW11 24668 2475 1975 54678 8438
EP300-FOXN1-FZD6 2964 2284 38649 17089 43579 EP300-FRZB-FZD1 35048 46610 23256 469 13611
EP300-FOXN1-LRP5 4494 2900 43340 32353 1904 AXIN1-EP300-FZD1 31915 846 24550 32377 43633
EP300-PORCN-PPP2R1A 9705 56176 25373 738 50930 EP300-FZD2-WNT4 7958 30171 46102 282 28923
AXIN1-EP300-WNT3A 29773 11569 2079 55580 29836 EP300-FZD2-TCF7L1 16132 9911 19549 19635 28746
AES-EP300-WNT2 41014 49014 5733 12100 31675 EP300-FZD2-PITX2 21066 1261 6278 52068 50788
DVL1-EP300-TCF7L1 52409 38334 12684 54201 14361 AES-EP300-KREMEN1 46085 42522 27876 8199 46619
EP300-FZD2-LEF1 22014 24731 6164 1694 20705 EP300-PORCN-WNT2B 15830 18382 7434 20043 39500
AXIN1-EP300-LRP6 48971 2895 29183 50900 39151 DVL1-EP300-PITX2 56689 28520 27891 57038 12113
DKK1-EP300-SENP2 8223 22887 7362 18319 12719 EP300-GSK3A-NLK 1488 36811 54049 43805 46079
EP300-FBXW11-SENP2 28012 28278 53048 10057 32539 EP300-FOXN1-WNT2B 3438 4494 43475 1580 25168
EP300-FBXW11-FBXW4 40244 31834 28900 400 16176 EP300-FGF4-PPP2R1A 434 56284 13608 15792 27194
FZD5-CCND1-EP300 14768 7896 41900 37382 55614 EP300-JUN-PPP2R1A 5997 52619 15125 40032 31600
EP300-FOXN1-RHOU 1535 1411 47672 37234 19244 EP300-FOXN1-WNT4 1123 1458 56189 3851 27498
EP300-GSK3B-LRP5 26984 34947 6303 3091 5561 AXIN1-EP300-WNT5A 45393 1954 35430 55047 50435
EP300-NKD1-WNT2 39516 745 54249 16318 30610 AXIN1-EP300-WNT4 36955 1563 18777 20017 24055
EP300-GSK3B-FBXW4 22624 38473 17932 6602 3482 AXIN1-EP300-PITX2 56749 23129 25963 57120 24869
EP300-FOXN1-GSK3B 2642 3165 56576 55942 32657 EP300-PORCN-TCF7L1 21837 509 26965 44207 37905
EP300-LRP6-SFRP4 2105 53738 39562 38275 32599 EP300-GSK3A-WNT2B 1984 14463 31882 45984 24146
Table 2: Rankings o EP300-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
6.3.4. Examining he beha iou o WNT-EP300-X combina ions
Sun e al. [16] epo ha he ansc ip ional coac i a o p300 in e ac s wi h β-ca enin
in i o and in i o and is c i ical o β-ca enin-media ed neoplas ic ans o ma ion.
9
