supplementary information - chapter 5 d.pdf · supplementary information - chapter 5 201. d...

DSupplementary Information - Chapter 5

201

DDDDDDDDDD

Appendix D

d.1 description of network properties

By focusing on the topological properties, our knowledge of the behavior of theproteins in a protein-protein interaction network can be increased. NetworkAnal-yser in Cytoscape is able to compute a range of topological features over a givenset of protein-protein interactions (Assenov et al., 2008; Doncheva et al., 2012).Some of these properties provide information about the direct neighborhood of aprotein (local property), while others provide information about the role of theproteins in the global network (global property). These features -which are usedfor analysis in this study- are briefly described below:

• The degree of a protein indicates the number of interactions the protein haswith other proteins in the network. Proteins with a high degree are alsoknown as hub genes and are suggested to have an important role in theregulation of the system (local property) (Diestel, 2005).

• The clustering coe�cient reflects the degree of connectivity between neigh-boring proteins. It is a ratio of the number of observed interactions betweenall neighbors of a protein divided by the maximum number of possible inter-actions between the neighbors of the protein. A high clustering coe�cientindicates a tight connected local network (local property) (Watts & Strogatz,1998; Barabasi & Oltvai, 2004).

• Betweenness centrality is a measure for the amount of control that a pro-tein exerts over all other proteins in the network and is calculated on basisof the number of shortest paths going through the given protein. A highbetweenness indicates a more important role of the protein in the networkorganization (global property) (Yoon et al., 2006).

• Eccentricity is the maximum length of the shortest path between a proteinand any other protein in the network. It is an indicator of the location ofthe node in the network. The more a protein is in the periphery, the higherthe eccentricity (global property).

• Closeness centrality is an indicator for the speed of spreading informationfrom a given protein to every other protein in the network. A protein witha high closeness is on average close to other proteins in the network (globalproperty) (Newman, 2005).

203

Appendix D

• Radiality of a protein is a measure that reflects the centrality of the proteinand is a measure of the number of shortest paths that goes through a proteincompared to all other proteins in the network. A radiality higher than theaverage radiality of the network indicates that the protein is in proximityto other proteins, where proteins with a lower radiality indicates tend to belocated in the periphery (global property) (Brandes, 2001).

• Stress of a protein indicates the number of shortest paths of all proteins inthe network that pass the protein. The higher this number, the bigger therole of the protein in given network (global property) (Brandes, 2001).

• The topological coe�cient is a relative measure to indicate the extent towhich a protein shares interacting partners with other proteins (global prop-erty) (Stelzl et al., 2005).

Distribution of Gene Size (corrected data)

Gene Size (corrected data)

Freq

uenc

y

0 200000 400000 600000 800000 1000000 1400000

050

0010

000

1500

0

Distribution of Exon Size

Exon Size

Freq

uenc

y

0 20000 40000 60000 80000 100000 120000

050

0010

000

1500

0

Figure D.1 Distribution plots [continues on next page]

204

DDDDDDDDDD

Appendix D

Distribution of # Unique Exons (corrected data)

# Unique Exons (corrected data)

Freq

uenc

y

0 5 10 15 20

050

010

0015

00

Distribution of # isoforms

# isoforms

Freq

uenc

y

0 10 20 30 40 50 60

020

0040

0060

0080

00Distribution of # expressed tissues

# expressed tissues

Freq

uenc

y

0 10 20 30 40

050

010

0015

00

Distribution of Sequenced Exon Size

Sequenced Exon Size

Freq

uenc

y

0 5000 10000 15000 20000 25000

010

0020

0030

0040

00

Distribution of Common Variants (corrected data)

Common Variants (corrected data)

Freq

uenc

y

0 10 20 30 40 50

050

010

0015

0020

0025

0030

00

Distribution of Rare Variants (corrected data)

Rare Variants (corrected data)

Freq

uenc

y

0 20 40 60 80 100

050

010

0015

00


205

Appendix D

Distribution of Non−Synonymous Variants (corrected data)

Non−Synonymous Variants (corrected data)

Freq

uenc

y

0 5 10 15

020

0040

0060

0080

0010

000

1200

0

Distribution of Missense Variants (corrected data)

Missense Variants (corrected data)Fr

eque

ncy

0 20 40 60 80 100

050

010

0015

00

Distribution of Splice Variants (corrected data)

Splice Variants (corrected data)

Freq

uenc

y

0 10 20 30 40 50

050

0010

000

1500

0

Distribution of Degree

Degree

Frequency

0 500 1000 1500

02000

4000

6000

8000

10000

12000

Distribution of Clustering Coefficient

Clustering Coefficient

Freq

uenc

y

0.0 0.2 0.4 0.6 0.8 1.0

010

0020

0030

0040

0050

00

Distribution of Betweenness Centrality

Betweenness Centrality

Freq

uenc

y

0.0 0.2 0.4 0.6 0.8 1.0

020

0040

0060

0080

0010

000

1200

014

000


206

DDDDDDDDDD

Appendix D

Distribution of Eccentricity

Eccentricity

Frequency

2 4 6 8 10

02000

4000

6000

8000

Distribution of Closeness Centrality

Closeness Centrality

Freq

uenc

y

0.2 0.4 0.6 0.8 1.0

050

010

0015

0020

0025

0030

00Distribution of Radiality

Radiality

Frequency

0.5 0.6 0.7 0.8 0.9 1.0

0500

1000

1500

Distribution of Stress

Stress

Frequency

0e+00 1e+08 2e+08 3e+08 4e+08 5e+08

02000

4000

6000

8000

10000

12000

Distribution of Topological Coefficient

Topological Coefficient

Freq

uenc

y

0.0 0.2 0.4 0.6 0.8 1.0

050

010

0015

0020

0025

00

Figure D.1 Distribution plots

207

Appendix D

020000

40000

60000

Gene Size (corrected data)

Essential Mono Complex Non−Associated

02000

4000

6000

8000

10000

Exon Size


02

46

810

# Unique Exons (corrected data)


24

68

1012

# Isoforms


010

2030

40

# Expressed Tissues


01000

2000

3000

4000

Sequenced Exon Size


Figure D.2 Boxplots [continues on next page]

208

DDDDDDDDDD

Appendix D

02

46

810

Common Variants (corrected data)


010

2030

40

Rare Variants (corrected data)


0.0

0.2

0.4

0.6

0.8

1.0

1.2

Non−Synonymous Variants (corrected data)


05

1015

2025

30Missense Variants (corrected data)


−1.0

−0.5

0.0

0.5

1.0

Splice Variants (corrected data)


020

4060

80

Degree



209

Appendix D

0.0

0.1

0.2

0.3

0.4

Clustering Coefficient


0e+00

1e−04

2e−04

3e−04

4e−04

Betweenness Centrality


5.0

5.5

6.0

6.5

7.0

7.5

8.0

Eccentricity


0.20

0.25

0.30

0.35

0.40

Closeness Centrality


0.70

0.75

0.80

0.85

Radiality


0500000

1000000

1500000

2000000

2500000

Stress



210

DDDDDDDDDD

Appendix D

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Topological Coefficient


Figure D.2 Boxplots for each gene characteristicfor each of the gene classes (corrected data). Thewidth of the boxplots indicates the size of the geneclass. Note: an IQR of zero will result in only ahorizontal line that indicates the median for thegene class. This is the case for ’non-synonymousvariant’, ’splice variants’ and ’eccentricity’.

211

Appendix D

Tabl

eD

.1C

orre

latio

nta

ble

onth

eda

taco

llect

edon

the

19di

�ere

ntch

arac

teri

stic

s.M

oder

ate

(ant

i-)co

rrel

atio

ns(>

=0.

4-

<0.

7)ar

ein

dica

ted

inor

ange

and

stro

ngco

rrel

atio

ns(

>=

0.7)

are

indi

cate

din

gree

n.

Gen

eSi

ze1

Exo

nSi

ze0.

641

#E

xons

0.66

0.58

1

#E

xpre

ssed

Tis

sues

0.11

0.11

0.12

1

#Is

ofor

ms

0.34

0.28

0.48

0.11

1

Sequ

ence

dE

xon

Size

0.58

0.64

0.69

0.08

0.24

1

Rar

eV

aria

nts

0.43

0.48

0.57

0.01

0.17

0.86

1

Com

mon

Var

iant

s0.

260.

290.

37-0

.06

0.06

0.62

0.73

1

Mis

sens

eV

aria

nts

0.35

0.39

0.48

-0.0

10.

110.

760.

920.

761

Non

-Syn

Var

iant

s0.

030.

010.

09-0

.04

-0.0

20.

190.

310.

300.

351

Splic

eV

aria

nts

0.12

0.04

0.22

-0.0

50.

050.

160.

230.

210.

240.

191

Deg

ree

0.07

0.08

0.19

0.17

0.16

0.12

0.01

-0.0

6-0

.07

-0.1

3-0

.06

1

Clu

ster

ing

Coe

�ci

ent

0.05

0.06

0.10

0.11

0.06

0.08

0.01

-0.0

3-0

.02

-0.0

6-0

.03

0.52

1

Bet

wee

nnes

s0.

060.

070.

170.

130.

150.

100.

00-0

.06

-0.0

7-0

.13

-0.0

50.

910.

351

Ecc

entr

icit

y-0

.06

-0.0

7-0

.15

-0.1

4-0

.11

-0.1

1-0

.03

0.03

0.03

0.09

0.06

-0.6

5-0

.29

-0.5

91

Clo

sene

ss0.

100.

120.

190.

190.

140.

140.

02-0

.05

-0.0

5-0

.13

-0.0

70.

800.

460.

75-0

.72

1

Rad

ialit

y0.

100.

120.

190.

200.

140.

140.

02-0

.05

-0.0

5-0

.13

-0.0

60.

810.

460.

75-0

.71

1.00

1

Stre

ss0.

060.

070.

170.

150.

150.

110.

00-0

.06

-0.0

7-0

.13

-0.0

60.

920.

380.

99-0

.61

0.79

0.79

1

Top

olog

ical

Coe

�ci

ent

0.00

-0.0

1-0

.03

-0.0

5-0

.03

-0.0

30.

010.

020.

030.

030.

04-0

.10

0.21

-0.0

60.

19-0

.18

-0.1

8-0

.06

1

GeneSize

ExonSize

#Exons

#ExpressedTissues

#Isoforms

SequencedExonSize

RareVariants

CommonVariants

MissenseVariants

Non-SynVariants

SpliceVariants

Degree

ClusteringCoe�cient

Betweenness

Eccentricity

Closeness

Radiality

Stress

TopologicalCoe�cient212

DDDDDDDDDD

Appendix D

Tabl

eD

.2D

escr

iptiv

est

atis

tics

per

gene

clas

s(u

ncor

rect

edda

ta).

Ess

enti

alG

enes

Mon

ogen

icG

enes

nge

nes

mea

nsd

med

ian

IQR

nge

nes

mea

nsd

med

ian

IQR

gene

size

3473

1597

234

731

8498

1327

832

8216

737

3167

690

2813

430

exon

size

3473

4293

3484

3500

3122

3282

4182

3569

3368

3151

#un

ique

exon

s34

733.

62.

13.

33.

232

824.

02.

23.

73.

2#

isof

orm

s33

394.

74.

04.

04.

031

594.

64.

03.

04.

0#

expr

esse

dti

ssue

s29

0331

.212

.936

.020

.026

9929

.913

.735

.021

.0

sequ

ence

dex

onsi

ze30

7617

5617

2912

9113

5329

4218

2717

9013

5613

65#

com

mon

vari

ants

3076

2.6

2.2

2.2

2.5

2942

3.1

2.8

2.6

2.8

#ra

reva

rian

ts30

7618

.17.

617

.49.

429

4219

.78.

118

.89.

9#

non

syno

nym

ous

vari

ants

3076

0.2

0.5

0.0

0.0

2942

0.3

0.6

0.0

0.3

#m

isse

nse

vari

ants

3076

10.8

6.3

10.2

8.1

2942

12.5

6.8

12.0

8.7

#sp

lice

vari

ants

3076

0.1

0.5

0.0

0.0

2942

0.1

0.5

0.0

0.0

degr

ee31

6833

.874

.013

3028

1324

.755

.99

21cl

uste

ring

coe�

cien

t31

680.

126

0.16

70.

083

0.15

628

130.

128

0.18

60.

071

0.16

7be

twee

nnes

sce

ntra

lity

3168

0.00

10.

018

0.00

00.

000

2813

0.00

00.

001

0.00

00.

000

ecce

ntri

city

3168

6.6

0.7

71.

0028

136.

70.

77

1.00

clos

enes

sce

ntra

lity

3168

0.31

70.

053

0.31

80.

049

2813

0.31

30.

067

0.31

00.

048

radi

ality

3168

0.77

80.

044

0.78

60.

050

2813

0.77

20.

046

0.77

80.

051

stre

ss31

6822

9903

412

9758

2619

0093

1038

057

2813

1545

132

8475

956

8638

869

6556

topo

logi

calc

oe�

cien

t31

680.

137

0.14

50.

080

0.14

728

130.

156

0.15

50.

101

0.18

2

213

Appendix D

[Tab

leD

.2co

ntin

ued]

Des

crip

tive

stat

istic

spe

rge

necl

ass

(unc

orre

cted

data

.

Com

plex

Trai

tG

enes

Non

-Ass

ocia

ted

Gen

esn

gene

sm

ean

sdm

edia

nIQ

Rn

gene

sm

ean

sdm

edia

nIQ

R

gene

size

3872

3147

953

771

1574

426

097

1101

611

429

1988

964

6910

297

exon

size

3872

4714

3560

3988

3558

1101

630

5622

3925

0824

76#

uniq

ueex

ons

3872

3.8

2.1

3.6

3.0

1101

63.

62.

33.

23

#is

ofor

ms

3748

4.9

3.9

4.0

4.0

1084

53.

63.

23.

04

#ex

pres

sed

tiss

ues

3267

30.8

12.8

36.0

19.0

8932

30.7

12.6

35.0

19

sequ

ence

dex

onsi

ze32

4719

6918

0214

8014

8887

4212

1110

3795

796

2#

com

mon

vari

ants

3247

3.3

2.9

2.7

2.7

8742

3.6

3.5

2.7

3.7

#ra

reva

rian

ts32

4719

.87.

718

.99.

087

4220

.89.

619

.710

.9#

non

syno

nym

ous

vari

ants

3247

0.3

0.6

0.0

0.3

8742

0.4

0.9

0.0

0.5

#m

isse

nse

vari

ants

3247

12.8

6.7

12.3

8.3

8742

14.0

8.4

13.1

10.1

#sp

lice

vari

ants

3247

0.1

0.4

0.0

0.0

8742

0.2

1.0

0.0

0.0

degr

ee30

6819

.445

.56

1671

9515

.639

.85

13cl

uste

ring

coe�

cien

t30

680.

124

0.19

00.

061

0.16

771

950.

134

0.21

00.

048

0.18

3be

twee

nnes

sce

ntra

lity

3068

0.00

10.

018

0.00

00.

000

7195

0.00

10.

020

0.00

00.

000

ecce

ntri

city

3068

6.8

0.7

71

7195

6.8

0.7

70

clos

enes

sce

ntra

lity

3068

0.30

70.

058

0.30

70.

047

7195

0.30

50.

060

0.30

40.

047

radi

ality

3068

0.76

70.

045

0.77

40.

051

7195

0.76

40.

046

0.77

10.

052

stre

ss30

6810

3247

362

4351

344

725

3858

9971

9572

0008

5320

972

2052

021

4150

topo

logi

calc

oe�

cien

t30

680.

163

0.16

40.

104

0.21

571

950.

173

0.17

40.

113

0.23

4

214

DDDDDDDDDD

Appendix D

Tabl

eD

.3W

ilcox

onRa

nkSu

mte

stre

sults

for

pair

-wis

eco

mpa

riso

nbe

twee

nth

ege

necl

asse

s(–

=8.

77e-

05).

Apo

sitiv

eZ-

scor

ein

dica

tes

that

gene

clas

sA

has

ahi

gher

rank

than

gene

clas

sB

and

ane

gativ

eZ-

scor

er

indi

cate

sth

atsa

mpl

eA

has

asm

alle

rra

nkth

ange

necl

ass

B.

Ess

enti

alvs

.M

onog

enic

Ess

enti

alvs

.C

ompl

exE

ssen

tial

vs.

Non

-Ass

ocia

tate

dZ-

scor

eP

-val

uer

Z-sc

ore

P-v

alue

rZ-

scor

eP

-val

uer

gene

size

*-2

.98

2.90

E-0

3-0

.047

-28.

10<

2.2E

-16

-0.3

8513

.79

<2.

2E-1

60.

115

exon

size

3.78

1.58

E-0

40.

059

-8.7

1<

2.2E

-16

-0.1

1926

.00

<2.

2E-1

60.

216

#un

ique

exon

s*-8

.47

<2.

2E-1

6-0

.133

-4.7

22.

34E

-06

-0.0

653.

494.

81E

-04

0.02

9#

isof

orm

s1.

152.

48E

-01

0.01

8-4

.58

4.61

E-0

6-0

.064

15.5

3<

2.2E

-16

0.13

0#

expr

esse

dti

ssue

s4.

143.

42E

-05

0.07

22.

292.

18E

-02

0.03

43.

416.

39E

-04

0.03

1

sequ

ence

dex

onsi

ze-2

.45

1.42

E-0

2-0

.041

-9.2

3<

2.2E

-16

-0.1

3719

.49

<2.

2E-1

60.

179

#co

mm

onva

rian

ts**

-9.4

0<

2.2E

-16

-0.1

57-1

2.53

<2.

2E-1

6-0

.186

-12.

29<

2.2E

-16

-0.1

13#

rare

vari

ants

**-1

0.83

<2.

2E-1

6-0

.181

-10.

51<

2.2E

-16

-0.1

56-1

4.01

<2.

2E-1

6-0

.129

#no

nsy

nony

mou

sva

rian

ts**

-9.4

2<

2.2E

-16

-0.1

57-9

.14

<2.

2E-1

6-0

.135

-12.

06<

2.2E

-16

-0.1

11#

mis

sens

eva

rian

ts**

-13.

65<

2.2E

-16

-0.2

28-1

4.98

<2.

2E-1

6-0

.222

-19.

90<

2.2E

-16

-0.1

83#

splic

eva

rian

ts**

-5.5

03.

86E

-08

-0.0

92-5

.71

1.12

E-0

8-0

.085

-1.3

31.

83E

-01

-0.0

12

degr

ee11

.74

<2.

2E-1

60.

198

18.9

7<

2.2E

-16

0.28

726

.06

<2.

2E-1

60.

256

clus

teri

ngco

e�ci

ent

3.91

9.19

E-0

50.

066

7.44

1.01

E-1

30.

113

8.65

<2.

2E-1

60.

085

betw

eenn

ess

cent

ralit

y10

.77

<2.

2E-1

60.

182

18.3

1<

2.2E

-16

0.27

727

.13

<2.

2E-1

60.

267

ecce

ntri

city

-8.9

4<

2.2E

-16

-0.1

51-1

3.26

<2.

2E-1

6-0

.201

-18.

22<

2.2E

-16

-0.1

79cl

osen

ess

cent

ralit

y10

.24

<2.

2E-1

60.

173

15.1

1<

2.2E

-16

0.22

917

.95

<2.

2E-1

60.

176

radi

ality

10.2

9<

2.2E

-16

0.17

415

.12

<2.

2E-1

60.

229

18.0

7<

2.2E

-16

0.17

8st

ress

10.5

0<

2.2E

-16

0.17

718

.18

<2.

2E-1

60.

275

25.7

8<

2.2E

-16

0.25

3to

polo

gica

lcoe

�ci

ent

-6.6

13.

87E

-11

-0.1

12-5

.53

3.22

E-0

8-0

.084

-6.4

98.

60E

-11

-0.0

64*c

orre

cted

for

exon

size

inba

sepa

irs;

**co

rrec

ted

for

sequ

ence

dex

onsi

zein

base

pair

s

215

Appendix D

[Tab

leD

.3co

ntin

ued]

Wilc

oxon

Rank

Sum

test

resu

ltsfo

rpa

ir-w

ise

com

pari

son

betw

een

the

gene

clas

ses

(–=

8.77

e-05

).A

posi

tive

Z-sc

ore

indi

cate

sth

atge

necl

ass

Aha

sa

high

erra

nkth

ange

necl

ass

Ban

da

nega

tive

Z-sc

ore

rin

dica

tes

that

sam

ple

Aha

sa

smal

ler

rank

than

gene

clas

sB

.

Mon

ogen

icvs

.C

ompl

exM

onog

enic

vs.

Non

-Ass

ocia

ted

Com

plex

vs.

Non

-Ass

ocia

ted

Z-sc

ore

P-v

alue

rZ-

scor

eP

-val

uer

Z-sc

ore

P-v

alue

r

gene

size

*-2

5.50

<2.

2E-1

6-0

.352

16.3

0<

2.2E

-16

0.13

641

.76

<2.

2E-1

60.

342

exon

size

-11.

80<

2.2E

-16

-0.1

6321

.92

<2.

2E-1

60.

183

34.2

5<

2.2E

-16

0.28

1#

uniq

ueex

ons*

3.18

1.48

E-0

30.

044

10.9

9<

2.2E

-16

0.09

28.

69<

2.2E

-16

0.07

1#

isof

orm

s-5

.54

3.06

E-0

8-0

.078

14.5

8<

2.2E

-16

0.12

321

.05

<2.

2E-1

60.

174

#ex

pres

sed

tiss

ues

-1.6

11.

08E

-01

-0.0

24-0

.71

4.80

E-0

1-0

.007

1.30

1.93

E-0

10.

012

sequ

ence

dex

onsi

ze-6

.92

4.56

E-1

2-0

.103

21.4

9<

2.2E

-16

0.19

928

.95

<2.

2E-1

60.

264

#co

mm

onva

rian

ts**

-3.7

61.

67E

-04

-0.0

56-4

.12

3.78

E-0

5-0

.038

-0.8

04.

23E

-01

-0.0

07#

rare

vari

ants

**-0

.32

7.47

E-0

1-0

.005

-4.1

23.

78E

-05

-0.0

38-4

.24

2.26

E-0

5-0

.039

#no

nsy

nony

mou

sva

rian

ts**

-0.7

44.

61E

-01

-0.0

11-3

.95

7.88

E-0

5-0

.037

-3.4

45.

73E

-04

-0.0

31#

mis

sens

eva

rian

ts**

-2.2

92.

23E

-02

-0.0

34-7

.89

2.91

E-1

5-0

.073

-6.1

01.

08E

-09

-0.0

56#

splic

eva

rian

ts**

-0.6

35.

31E

-01

-0.0

093.

741.

87E

-04

0.03

54.

526.

28E

-06

0.04

1

degr

ee8.

25<

2.2E

-16

0.12

715

.93

<2.

2E-1

60.

159

7.73

1.07

E-1

40.

076

clus

teri

ngco

e�ci

ent

3.53

4.14

E-0

40.

054

4.87

1.14

E-0

60.

049

1.52

1.29

E-0

10.

015

betw

eenn

ess

cent

ralit

y8.

36<

2.2E

-16

0.12

917

.52

<2.

2E-1

60.

175

9.23

<2.

2E-1

60.

091

ecce

ntri

city

-4.7

02.

61E

-06

-0.0

73-9

.62

<2.

2E-1

6-0

.096

-4.9

96.

01E

-07

-0.0

49cl

osen

ess

cent

ralit

y5.

311.

10E

-07

0.08

28.

37<

2.2E

-16

0.08

43.

141.

68E

-03

0.03

1ra

dial

ity5.

271.

38E

-07

0.08

18.

44<

2.2E

-16

0.08

43.

251.

15E

-03

0.03

2st

ress

8.36

6.48

E-1

70.

129

16.3

4<

2.2E

-16

0.16

38.

124.

44E

-16

0.08

0to

polo

gica

lcoe

�ci

ent

-0.1

68.

75E

-01

-0.0

02-1

.48

1.38

E-0

1-0

.015

-1.2

52.

12E

-01

-0.0

12*c

orre

cted

for

exon

size

inba

sepa

irs;

**co

rrec

ted

for

sequ

ence

dex

onsi

zein

base

pair

s

216

supplementary information - chapter 5 d.pdf · supplementary information - chapter 5 201. d...

Documents