A
B
1st
Pair 1
Pair 1
Pair 2
Pair 2
5th
Pair 3
Pair 3
2nd
Pair 4
Pair 4
3rd
Pair 5
Pair 5
4th
Pair 6
Pair 6
6th
C
Pair 1
Pair 2
1st
D
Edge style
1st
>19 label co-occurences
>9 label co-occurences
>4 label co-occurences
5th
>2 label co-occurences
2nd
Pair 3
2nd
3rd
4th
6th
Pair 4
3rd
Pair 5
4th
Pair 6
6th
Supplementary Figure 1. Estimating genome-wide distribution of label co-occurrences between gene modules.
(A) Ellipses represent gene modules, while green edges depict significantly similar gene modules. Number of label
co-occurrences between the modules are indicated by edge styles. Overlapping ellipses indicate which modules are
sharing genes, i.e. overlapping. (B) Module-pair collection is sorted according to the number of label co-occurrences,
with more similar module-pairs being collected first. (C) Here, the heuristic is determining overlapping modules, with
modules having more label co-occurrences having higher precedence over modules with less number of label
co-occurrences. For example, both modules in module-pair 2, and one module in module pair 6 are overlapping with
modules that have higher precedence. If at least one of the modules is not overlapping with modules of higher precedence, the label co-occurrence value is collected. (D) In this example, out of six module pairs, 5 label co-occurrence
values are collected. Note that the label co-occurrence value from pair 2 is disregarded, as both modules are overlapping with pair 1.
LOC_Os07g07690.2
LOC_Os01g37120.1
LOC_Os11g19810.1
LOC_Os06g43790.1
LOC_Os01g10150.2
LOC_Os03g13790.2
LOC_Os02g06720.1
LOC_Os07g46690.1
LOC_Os10g37480.2
LOC_Os02g54020.1
LOC_Os01g70810.1
LOC_Os11g29240.1
LOC_Os01g14370.2
LOC_Os03g02320.2
LOC_Os08g03360.1
LOC_Os11g06190.1
LOC_Os07g46590.1
LOC_Os11g18770.1
LOC_Os03g52794.1
LOC_Os03g19340.1
LOC_Os02g46450.2
LOC_Os02g52960.1
LOC_Os03g53960.1
LOC_Os09g33980.1
LOC_Os07g46690.1
LOC_Os02g52960.1
LOC_Os02g05450.1
LOC_Os01g49680.1
LOC_Os07g31340.1
LOC_Os11g43970.1
LOC_Os05g03550.1
LOC_Os07g25680.1
LOC_Os10g31970.1
LOC_Os09g04890.1
LOC_Os07g46590.1
LOC_Os07g46590.1
LOC_Os02g01740.1
LOC_Os06g17840.1
LOC_Os07g25710.4
LOC_Os06g43790.1
A
LOC_Os09g04890.1
LOC_Os02g32570.1
LOC_Os02g19860.1
LOC_Os11g19810.2
LOC_Os02g34630.1
LOC_Os11g19810.2
LOC_Os03g19530.1
LOC_Os10g38850.1
LOC_Os01g62500.1
LOC_Os04g42320.1
LOC_Os01g09760.1
LOC_Os02g32570.1
LOC_Os02g17190.1
LOC_Os11g18770.2
LOC_Os06g01320.1
LOC_Os02g06500.1
LOC_Os08g03360.1
LOC_Os05g05810.1
LOC_Os08g24760.1
LOC_Os01g48180.1
LOC_Os04g40090.1
LOC_Os03g53880.1
LOC_Os07g31450.1
LOC_Os03g11470.1
LOC_Os07g44210.1
LOC_Os11g06190.1
LOC_Os01g49680.1
LOC_Os07g09580.1
LOC_Os01g22390.2
LOC_Os03g51220.1
LOC_Os02g39920.1
LOC_Os01g39250.1
LOC_Os07g46590.1
LOC_Os02g46450.2
LOC_Os04g28090.1
LOC_Os03g53630.1
LOC_Os01g40980.1
LOC_Os02g15220.2
LOC_Os09g33980.1
LOC_Os02g49090.1
LOC_Os02g05450.1
LOC_Os06g14412.1
LOC_Os06g43840.1
LOC_Os01g68120.1
LOC_Os06g19660.1
LOC_Os07g48270.1
LOC_Os05g05230.1
LOC_Os03g15580.1
LOC_Os02g11760.1
LOC_Os08g19590.2
LOC_Os07g45064.1
LOC_Os04g52020.1
LOC_Os03g43800.2
LOC_Os02g46450.2
LOC_Os02g02050.1
LOC_Os04g01970.1
LOC_Os02g47900.1
LOC_Os02g02290.1
LOC_Os03g14980.2
LOC_Os04g14510.2
LOC_Os08g12680.1
LOC_Os06g01320.1
LOC_Os02g06720.1
LOC_Os03g22900.1
LOC_Os12g41900.1
LOC_Os07g07690.1
LOC_Os01g36860.1
LOC_Os03g53720.2
LOC_Os01g33800.1
LOC_Os01g33800.1
LOC_Os01g49940.2
LOC_Os10g42439.1
LOC_Os01g73410.1
LOC_Os03g28310.1
LOC_Os10g37730.3
LOC_Os07g06950.1
LOC_Os04g52040.1
LOC_Os12g30540.1
LOC_Os04g52040.1
LOC_Os11g28365.1
LOC_Os03g56630.1
LOC_Os02g34590.1
LOC_Os01g56800.1
LOC_Os01g62820.1
LOC_Os01g71770.1
LOC_Os07g28260.1
LOC_Os03g62640.3
LOC_Os02g54120.4
LOC_Os10g33874.1
LOC_Os10g42710.1
LOC_Os10g42710.1
LOC_Os01g62650.1
LOC_Os10g31970.1
LOC_Os01g15630.2
LOC_Os02g24134.1
LOC_Os02g24134.1
LOC_Os02g05880.1
LOC_Os08g08000.1
LOC_Os10g35220.1
LOC_Os02g39550.3
LOC_Os01g62650.1
LOC_Os07g49260.1
LOC_Os09g36090.1
LOC_Os01g03070.1
LOC_Os04g18010.1
LOC_Os01g27150.1
LOC_Os10g35220.1
LOC_Os02g39550.3
LOC_Os02g05880.1
LOC_Os05g09630.2
LOC_Os04g48370.1
LOC_Os03g11240.1
LOC_Os08g05940.1
LOC_Os02g05880.1
LOC_Os02g01170.1
LOC_Os03g42050.1
LOC_Os04g18010.1
LOC_Os02g39300.1
LOC_Os04g18010.1
LOC_Os04g18010.1
LOC_Os05g09630.1
LOC_Os02g48010.1
LOC_Os03g35340.1
LOC_Os05g09630.2
LOC_Os03g11240.1
LOC_Os04g52040.4
LOC_Os04g52074.1
LOC_Os02g01170.1
LOC_Os05g06690.2
LOC_Os07g43030.1
LOC_Os04g18030.2
LOC_Os03g35340.1
LOC_Os02g46450.2
LOC_Os02g33750.2
LOC_Os01g72320.1
LOC_Os02g48010.1
LOC_Os02g18370.1
AAA
ABC2_membrane
ABC_tran
LOC_Os03g01250.1
Acetyltransf_1
LOC_Os10g36810.1
Amino_oxidase
LOC_Os08g39310.1
Beach
LOC_Os07g07250.1
Bromodomain
LOC_Os03g44900.1
Chromo
LOC_Os03g52594.3
DAO
LOC_Os08g20610.1
DDT
LOC_Os04g14130.3
DEAD
LOC_Os10g35760.2
LOC_Os10g41590.1
LOC_Os04g39629.1
DEAD_2
LOC_Os05g43280.1
LOC_Os07g20510.1
LOC_Os03g04520.4
LOC_Os08g37960.2
LOC_Os01g63940.1
LOC_Os02g11750.1
LOC_Os08g32100.1
DIRP
LOC_Os08g41530.1
DSHCT
LOC_Os03g09260.1
DUF1605
LOC_Os03g09260.1
DUF2075
LOC_Os03g06950.1
DUF2081
LOC_Os12g40520.1
LOC_Os05g51550.1
LOC_Os01g26940.1
LOC_Os01g56490.1
DUF3351
DUF3591
LOC_Os05g05700.2
DUF605
LOC_Os01g49940.1
DUF699
FAD_binding_2
LOC_Os07g23110.1
FAT
LOC_Os04g57640.2
FATC
B
FYRC
LOC_Os03g12236.1
FYRN
BRCT
LOC_Os03g12236.3
FtsH_ext
PADR1
LOC_Os01g27740.3
GSPII_E
PARP
Transposase_24
NTP_transf_2
PAP_assoc
Mem_trans
NABP
PPR
TK
PUF
PAP_central
DUF3444
DUF3752
DnaJ
ORTHO005661
KH_1
RVT_1
LUC7
DnaJ_CXXCXGXG
Ank
MIP-T3
PARP_reg
GYF
CG-1
PWI
RRM_1
RST
Plus-3
TIG
WGR
SWIB
PCI
RPN7
HA2
ORTHO001900
eIF3_N
Homeobox
IstB
zf-PARP
KTI12
Zeta_toxin
DUF3223
RNA_pol_Rpb1_1
RNA_pol_Rpb1_2
RNA_pol_Rpb1_3
Cullin
Cullin_Nedd8
FYVE
RCC1
RNA_pol_Rpb1_5
KAT11
CRM1_C
DUF627
DZC
Exo_endo_phos
Cse1
DUF629
LETM1
MATH
UCH
zf-C3HC4
DUF3453
Symplekin_C
TFIID_20kDa
ORTHO005269
ORTHO002454
ORTHO026427
IBN_N
Xpo1
zf-UBP
RNA_pol_Rpb1_7
HIRAN
Helicase_C
WWE
BicD
HDA2-3
KaiC
LBR_tudor
PAZ
Myb_DNA-binding
PB1
PDR_assoc
PHD
PI3_PI4_kinase
PWWP
Peptidase_M41
FAR1
MULE
SWIM
Sec1
HECT
ORTHO013207
NOT2_3_5
Not3
Pkinase
Pkinase_Tyr
Pre-SET
Pyr_redox
Pyr_redox_2
Rad17
ResIII
Supplementary Figure 2. An example of large gene modules involved in chromatin remodeling in rice. (A) Two gene modules from rice with loc_os10g31970 and loc_os02g46450 used as
module centers (large nodes). The nodes represent label co-occurrences, while node labels
represent genes assigned to the label co-occurrences. Gray edges represent associations of the
label co-occurrences to the module centers. The two modules are overlapping to some degree and
consequently share genes, shown by red dashed edges. The number of dashed edges is equal to
the number of genes shared between the label co-occurrences. (B) Labels found in the label
co-occurrences. For simplicity, only pfam labels are shown. The two modules show enrichment in
ontologies representing transcription factors, chromatin remodeling/structure factors, signaling and
cell division. The ontology analysis for both modules can be viewed at http://aranet.mpimpgolm.mpg.de/responder.py?name=gene!osa!13835 and http://aranet.mpimpgolm.mpg.de/responder.py?name=gene!osa!8427
Ribonuclease_3
SET
SNF2_N
SRP54
START
SWIRM
Sec63
TBP-binding
Thi4
UBA
UPF1_Zn_bind
UvrD-helicase
Viral_helicase1
WD40
ZZ
dsRNA_bind
ubiquitin
zf-TAZ
B
A
B
A
D
C
E
C3136
C3136
C4148
C3114
C1310
C1310
EB439252
C3197
C3152
C1787
C8837
C3061 EB677962
C1736
C1736
C8649
C4569
C2940
C11224 C8718
C10632
C3070
C972
C4712
C4712
C10885
C1859
C9924 C1561
C3738
C4910
C980
C8393
C1848
DV158444 C9924
C1368
C5219
C11419
C1434
C1279
B
C
A
D
C1866
C1471
C8485
C1471
C3280
C938
BP527539
C5584
C8219
C11613
C348
C2112
C1214
C11576
C8310
C11403
C11403
C3247
C952
C4312
BP532252
C10137
C10485
C8934
C9851
C1094
EB449228
C8473
EB682713
C1349
C1454
C5868
BQ842822
C8402
CV018266
C3296
C5517
C5517
C10796
C112
C9568
EB682713
C112
C3196
C9568
C10306
C5289
C1067
C152
C1067
C1465
E
C4448
C8061
C974
C885
C885
C2986
BP531531
C5850 C11280
C3788 BP133193
CV016707
C3231 C7609
C101
C1462
C3368
C1191
CV019867
C4478
C1882
C3089
C1882
CV018824
C3143
CV016257
CV019619
C8088
C8326
C1349
C4421
C2743
C8588
C3654
C8768
C8137
C237
C8137
CV020400
C901
C1259
CV021641
C1769
DV159355 C3283
C3147
C8240
C2498
C4891
C210
BP192665
C1893
C210
C8818
CV020678 C8763
C1676
C5897
EB683044
EB431978
BP531527
BP531527
C
Ribosomal_S13_N
Ribosomal_L30
Ribosomal_L30_N
Ribosomal_L35Ae
Ribosomal_L37ae
KH_2
Ribosomal_S3_C
Ribosomal_S8e
Ribosomal_S30
Ribosomal_S7e
Ribosomal_S25
RS4NT
Ribosomal_S4
Ribosomal_S4e
S4
Ribosomal_S17e
Ribosomal_S26e
Ribosomal_S19e
Ribosomal_L7Ae
Ribosomal_L37e
Ribosomal_L39
Ribosomal_S2
Cpn60_TCP1
Ribosomal_60s
Ribosomal_L10
Ribosomal_S9
Ribosomal_S15
Ribosomal_L5
Ribosomal_L5_C
Nop10p
Ribosomal_L18e
Porin_3
Ribosomal_S5
Ribosomal_S21e
Ribosomal_S27e
Ribosomal_S12
Ribosomal_S13
Ribosomal_L14
Rad60-SLD
Ribosomal_L40e
Ribosomal_S27
ubiquitin
Ribosomal_L22e
Ribosomal_S8
Ribosomal_L13e
KOW
Ribosomal_L27e
Ribosomal_S5_C
WD40
eIF2A
NAC
UBA
Supplementary Figure 10. An example of large gene modules involved in ribosome biosynthesis in tobacco.
(A) To make comparisons of gene module content easier, the co-expression networks are simplified by collecting all
genes belonging to one label co-occurrence and representing it as one node. In this example, genes B and C
belong to same label co-occurrence (green node) and are assigned to the same node in simplified network. (B) Two
gene modules from tobacco with C1368 and C1349 used as module centers (large nodes). The nodes represent
label co-occurrences, while node labels represent genes assigned to the label co-occurrences. Gray edges represent associations of the label co-occurrences to the module centers. The two modules are weakly overlapping and
consequently sharing genes, which is shown by connecting the overlapping label co-occurrences by red dashed
edges. (C) Labels found in the label co-occurrences. For simplicity, only pfam labels are shown. The two modules
show enrichment in ontologies representing ribosome structural components.
A
d=2
d=2
B
A
d=1
d=4
F
d=1
d=2
d=2
d=2
A
2nd
B
3rd
4th
C
d=2
d=2
A
D
C
C
E
B
2nd
d=2
d=1
B
E
3rd
4th
C
d=2
d=4
D
1st
5th
6th
F
d=1
d=1
d=4
D
1st
E
5th
6th
F
d=1
Supplementary Figure 4. Estimating the distribution of representative module degrees.
(A) Nodes represent modules, and edges indicate similar modules. Numbers adjacent to a module
indicate the degree (d) of a module. (B) Module collection is determined by module degree, with modules
with higher degree having higher precedence. (C) The first module, with highest degree is collected
(module D), together with its neighbors (modules B, C,E and F). Modules can only be collected once. In
this example, out of six modules, two module degrees were collected (d=2, d=4 for modules A and D).
A
HW09A20u_at
Contig18367_at
Contig9885_at
Contig9764_at
Contig6333_at
Contig6238_s_at
Contig2249_at
Contig12071_at
rbags1c11_at
Contig15264_at
Contig8958_at
Contig6546_at
Contig6009_at
Contig5838_at
Contig7171_s_at Contig14304_at rbah38o04_s_at
Contig9632_at
HW01L24u_at
HV_CEb0004O15r2Contig21968_at Contig23141_at Contig17921_at
Contig2425_s_at
GST_N
GST_C
ADH_N
ADH_zinc_N
p450
UDPGT
3Beta_HSD
Epimerase
Chitin_bind_1
Glyco_hydro_19
WRKY
peroxidase
Bet_v_1
FMN_red
Flavodoxin_1
Oxidored_FMN
Peptidase_C1
B
Glyma09g0673 Glyma09g3629 Glyma06g1137 Glyma12g3576 Glyma13g3957 Glyma03g0775 Glyma12g0895 Glyma12g3568 Glyma20g1997
Glyma12g3053 Glyma06g0037 Glyma12g0759 Glyma11g1172 Glyma15g0390 Glyma07g1827 Glyma14g0067 Glyma13g1944 Glyma19g3719
Glyma14g1140 Glyma20g3567 Glyma07g0023 Glyma15g1797 Glyma03g3390 Glyma11g1015 Glyma11g0078 Glyma07g1827
RNA_pol_Rpb1
SNF2_N
RRM_1
NTF2
Pre-SET
SET
YDG_SRA
Frigida
Homeobox
PHD
DDT
FF
WW
BTAD
Coatomer_E
TPR_1
TPR_2
DEAD
Helicase_C
DUF1605
WD40
PX
SMC_N
SMC_hinge
GYF
Supplementary Figure 5. Examples of frequently multiplied modules in plants.
Genes/probesets that were used as module centers are indicated above the boxes. Colored shapes indicate label
co-occurrences that were present in the respective modules. For simplicity, only pfam labels are shown.
(A) Metabolism related modules in barley. (B) Transcription related modules in soybean.
B
A
Wild type
cobl10-4qrt1-2
C
D
pir1-1
E
crd1-1
pPIR1::GUS
Supplementary Figure 6. Mutants from the pollen cell wall module show normal pollen.
(A-D) Whole anthers and mature pollen (inset upper right) stained with Alexander stain and DAPI (insets lower
left) indicate that pollen viability is not affected in the mutants. Note that cobl10-4 was crossed into the quartet
(qrt)1-2 background, which displays tetrads of pollen grains after meiosis (Francis et al., 2006). (E) Pollination of
wild type pistils with pPIR::GUS pollen shows pollen and pollen tube specific expression of PIR1.
Scale bars: 50 µm (including insets).
Mature root
Mature seed
Senescence leaf
Mature leaf
Lower stem
Upper stem
Closed buds
Open buds
Flower
Young leaf
Young silique
Log2
-2
2
Rt9.57_409
Rt10.22_439
Rt18.07_623
Rt21.59_540
Rt14.32_1169
Rt21.16_521
Rt14.24_1096
Rt15.57_1226
Rt19.30_934
Rt20.04_915
Rt22.15_566
Rt9.89_489
Rt9.93_443
Rt10.84_439
Rt11.97_1854
Rt13.56_245
Rt13.13_361
Rt14.68_1312
Rt12.44_822
Rt14.49_339
Rt13.75_339
Rt19.20_343
Rt8.28_205_Trp
Rt11.17_757_putative anthocyanin
Rt12.57_609_KGG
Rt13.84_303.6_N_
Rt14.90_287.3_N_
Rt5.81_251.4_N_
Rt10.60_472.7_P_
Rt10.61_470.4_F_
Rt11.03_468.7_F_
Rt8.81_468.6_F_
Rt13.50_787.3_P_
Rt9.70_466.5_F_
Rt14.57_568.7_P_
Rt14.95_566.8_P_
Rt16.41_585.4_P_
Rt13.11_463.7_Q3G
Rt15.08_1130
Rt12.44_1850
Rt13.63_447_K3G
Rt18.81_669
Rt11.66_353_4CGA
Rt14.05_852
Rt14.44_981_putative Nicotianoside III
Rt14.68_878
Rt14.77_989
Rt10.34_472
Rt10.76_470
Rt11.00_470
Rt13.88_1416
Rt13.20_593_K-3G6
''R
Rt15.91_1023
Rt16.16_1174
Rt15.71_1256
Rt15.47_1169_putative Nicotianoside VII
Rt15.72_1114
Rt16.10_1154_putative Nicotianoside V
Rt10.13_472
Rt11.54_486
Rt17.05_1112_putative Nicotianoside
Rt16.25_1109_putative Nicotianoside
Rt16.32_821
Rt16.59_1008_putative Nicotianoside II
Rt16.78_862
Rt17.14_948
Rt16.99_1094_putative Nicotianoside
Rt17.49_948
Rt11.60_540
Rt13.56_292
Rt10.41_453
Rt9.38_442
Rt13.64_1071
Rt9.80_428
Rt13.18_438
Rt14.23_912_putative Nicotianoside C
Rt14.23_458
Rt14.04_895
Rt15.45_964
Rt8.12_367
Rt15.68_309
Rt11.13_353_5CGA
Rt9.48_353_3CGA
Rt10.07_658
Rt14.89_275
Rt15.49_805
Rt16.31_806
Rt12.93_434
Rt17.77_332
Rt23.08_730
Rt12.70_609_Q-3G6
Rt12.18_625_QGH ''R
Rt13.27_623_putative flavonol glycoside
Rt17.74_329
Rt20.82_669
Rt21.55_683
Rt22.26_697
Rt22.29_724
Rt15.04_878
Rt12.39_363
Rt20.01_682
Rt20.11_655
Rt20.81_696
Rt21.53_710
Rt23.76_744
Supplemental Figure 7. Hierarchical clustering analysis of LC-MS metabolite profile of tobacco tissues.
Relative peak area was normalized by average value and shown with logarithmic scale (log2). Fold change is visualized by indicating color, red (high) and blue (low), respectively.
A
Tobacco
cv019175_at
Arabidopsis
at1g21130
Tobacco
c3748_at
Tobacco
c3748_x_at
Arabidopsis
at1g21100
Tobacco
eb427179_s_at
Arabidopsis
at5g53810
Arabidopsis
at1g76790
Arabidopsis
at5g37170
Tobacco
eb684248_at
Arabidopsis
at5g54160
B
C
bp526622
at2g45580
at3g44250
c1929
c1929
c9871
c9087
at5g38130
eb442153
at1g61680
at2g24210
c9087
eb427243
c9871
eb442153
at4g39480
at1g66120
at1g22380
at5g53810
dw000847
c533
eb427179
eb426591
at1g66540
at3g53300
c1918
c9610
c1998
c8891
eb427179
c11505
bp527611
c9377
eb427315
c533
at5g37170
c5971
dw000243
eb428900
bp530950
c493
at1g65450
c4917
eb426013
at3g25810
c493
c658
at5g38120
c9210
c6423
Module: 11
c4106
cv019608
Module: Query gene
HOM000005
HOM000093
ORTHO000744
ORTHO000866
ORTHO014107
ORTHO025893
p450
HOM000066
ORTHO000740
ORTHO002190
Prenyltrans
Terpene_synth
Terpene_synth_C
Glyco_transf_28
HOM000023
ORTHO000038
UDPGT
HOM000062
HOM000359
ORTHO012960
ORTHO046158
Transferase
AMP-binding
HOM000212
HOM000226
ORTHO001435
ORTHO002921
Dimerisation
HOM000097
Methyltransf_2
ORTHO046399
ORTHO232858
Supplementary Figure 8. EB427179-like gene modules in Arabidopsis. A) Gene module network of
EB427179 with Arabidopsis modules shown. B) Expression profile of At5g53810. C) Gene module comparison of EB427179 and At5g53810 and At5g37170.
LSD pair found:
Within a module
Across two modules
Module B
Generated from perspective of gene 6
Similar to module A and E
Not in modules
6
Module A
Generated from perspective of gene 1
Similar to module B and E
1
Module C
Generated from perspective of gene 3
Similar to module D
(ii)
7
2
8
3
9
4
5
Module E
Generated from perspective of gene 5
Similar to module A and B
Module D
Generated from perspective of gene 9
Similar to module C
10
Gene 10
Does not form a module
Supplementary Figure 9. Genes can be present in multiple modules and have multiple LSD relationships.
Nodes represent genes, while black solid edges represent co-expression relationships. Node colors represent
different gene labels. Dashed edges represent the three LSD relationships. In this example, genes 2 and 4 can be
in the same module (module C), or in two similar modules (module A and E), depending on the investigated
module.
A
LSD pair found:
Across two modules
Within a module
Not in modules
Found:
2 across edges
1 within edge
2 not edge
Module X
Module Y
B
Found:
0 across edges
2 within edges
3 not edge
1st permutation
Module X
Module Y
Found:
3 across edges
0 within edges
2 not edge
2nd permutation
Module X
...
Module Y
Found:
1 across edges
1 within edges
4 not edge
1000th permutation
Module X
Module Y
Supplementary Figure 10. Counting and estimating the significance of large-scale duplicated genes
(LSD) in modules. (A) Consider two similar modules, X and Y, containing four genes each. Nodes and
node colors represent genes and labels, respectively. Red edges represent LSD pairs found across the two
modules. Gray edges represent LSD pairs found within a module, while blue edges represent LSD pairs
not found in two similar modules. In this example, 2 red edges, 1 gray edge and 2 blue edges (5 edges in
total) were found. Note that for simplicity, only the violet label is analyzed in this example. (B) To estimate
the significance of the edge distributions, the 5 LSD edges are distributed randomly among the members of
the violet label. The criteria are: the number of edges must stay constant (i.e. 5) and the edges can be only
distributed among the violet label. The LSD edges are permuted 1000 times, and the number of red, gray
and blue edges is counted for each permutation. The analysis is done for each label, if any LSD gene-pairs
are found for the label.