a b - springer static content server10.1186/gb-2004-5-5-r33... · cytoplasmic ribosomal small...
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Abf1 (37)
RNA polymerase II (13)
3
RNA polymerase III (13)
3
Azf1 (2)
Cdc28p complexes (10)
2
Bck2 (2)
2
Cbf1 (16)
Cytochrome bc1 complex (10)
2
Cln3 (2)
2
Dun1 (3)
Ribonucleoside diphosphate reductase (4)
3
Far1 (2)
2
Fau1 (3)
Glycine decarboxylase (4)
3
Gcn4 (40)
Anthranilate synthase (2)
22
Gcr1 (18)
Cytoplasmic translation elongation (9)
2
eEF1 (6)
2
Hap2 (14)
2-oxoglutarate dehydrogenase (3)
2
Hap3 (15)
2
Hap4 (14)
3
Hir1 (4)
Nucleosomal protein complex (8)
4
Hir2 (2)
2
Hir3 (3)
3
Hta1 (2)2
Hta2 (2)
2
Ime4 (1)
Ume6 Ime1 complex (2)
1
Ino2 (19)
Fatty acid synthetase cytoplasmic (2)
2
Ino4 (19)
2
Mbp1 (6)
2
Mcm1 (14)3
Pre replication complex (14)
2
Mig1 (26)
GAL80_complex (3)
2
Msn2 (56)
Alpha_alpha-trehalose-phosphate_synthase (4)
3
Msn4 (58)
3
Ndt80 (11)5
Rad26 (1)
1
Rad9 (2)
2
Rap1 (32) 2
Reb1 (19)
2
Rfx1 (5)
3
Rpn4 (11)
19-22S regulator (18)
6
20S proteasome (15)
2
Rtg1 (12)
Isocitrate dehydrogenase (2)
2
Rtg3 (6)
2
Sit4 (2) 2
Spt10 (3)
2
Spt16 (2)
2
Spt21 (3)
2
Stb1 (1)
MBF_complex (2)
1
SBF complex (2)
1
Swi4 (8)
2
Glucan synthases (5)
2
Swi6 (10)3
Tup1 (7)
3
Xbp1 (5)
3
Yhp1 (1)
1
Yku70 (2)
2
a b
c
Respiration chain complexes(37)
Figure S1 : Network graph built using statistically significant (E-value<0.1) overlaps between annotated complexes from the CYGD database and annotated regulons (see main manuscript for details).Complexes are denoted by their name in the CYGD database and regulons by the common name ofthe transcription factor which bind it.Each node represents a complex (red ellipses) or a regulon (blue rectangles). The number of genes ineach group (complex or regulon) is given in parentheses. The number of genes common to a givencomplex-regulon pair is indicated along the lines (arc) joining the pair. a,b,c clusters are detailed in themain manuscript.
Abf1 (282)
RNA polymerase III (13)
5
Bas1 (44)
Glycine decarboxylase (4)
3
Fhl1 (194)
cytoplasmic ribosomal large subunit (81)
67
cytoplasmic ribosomal small subunit (57)
53
Gal4 (40)
GAL80 complex (3)
2
Gat1 (1)
Dynactin complex (3)
1
Gcn4 (80)
Arginine-specific carbamoylphosphate synthase (2)
2
Hap2 (19)
Cytochrome bc1 complex (9)
2Cytochrome c oxidase (8)
2
Hap3 (23)
2
Hap4 (69)
78
F0 F1 ATP synthase (15)
10
Hir1 (30)
Nucleosomal protein complex (8)
6
Hir2 (21)
6
Ino2 (11)
Fatty acid synthetase cytoplasmic (2)
2
Ino4 (19)
2
Mbp1 (112)Cdc28p complexes (10)3
Mcm1 (89)
Alpha-agglutinin anchor (2)
2Pre-replication complex (14)3
Met4 (29)2
Pdr1 (69)
8
Rap1 (209)
46
30
Rfx1 (32)
Ribonucleoside diphosphate reductase (4)
3
Yap5 (107)
10
8
ab
2
Replication-complexes (49)
7
Replication-factor-A-complex (3)
Swi4 (136)
5
c
Figure S2 : Network graph built using statistically significant (E-value<0.1) overlaps between annotated complexes from the CYGD database and high-throughput regulons (see main manuscript for details).Notations are identical to figure S1. a,b,c clusters are detailed in the main manuscript.
CDC28
CLN1
CLN2
HMS407 (2/4)
TAP83 (3/10)
Cln3 (2/2)
Far1 (2/2)
Sit4 (2/2)Swi4 (2/8)
Spt16 (2/2)
Bck2 (2/2)
Swi6 (2/10)
b
SWI4RAD53
CLB2
CLB3
CLB5
HMS365 (2/18)
HMS468 (5/10)
HMS422 (2/7) HMS188 (2/2)Xbp1 (2/5)
Ndt80(2/11)
Mcm1 (3/14)
TPS1
ARA1
GRX1
TPS2
TRR1
TSA2
ADE6
YGR086C
ADE3
YAK1
SOD1
APE2UBA1
HSP104
AHP1
PGM2
ADE17
TPS3ADH2
DCS2
OYE3
GPH1
TAP31 (3/16)
HMS111 (3/10)
HMS210 (6/55)
HMS25 (3/26)
HMS26 (4/14)
HMS50 (5/45)
HMS84 (11/47)
Bas1 (3/17)
Msn2 (13/56)
Yap1 (8/32)Msn4 (13/58)
Pho2 (3/21)
d
Figure S3 : Detailed view of the genes linking clusters of protein complexes and high-throughputregulons. Each ellipse represents a high-throughput complex, which is denoted as detailed in the main manuscript. Regulons are surrounded by rectangles, and their intersections with complexes are displayed by rounded boxes.a) Permeases clusterb) Cyclin-protein kinase clusterc) Glycolysis, fermentation, and RNA polymerases clusterd) Stress response cluster
PGK1
TAP18 (2/3)
Sto1 (1/1)
Abf1 (8/37)
ENO2
Gcr1 (6/18)
Rap1 (7/32)
TPI1
ADH1
TAP139(6/43)
PDC1
HIS4
RPB2
SPT15
TDH3
FBA1
SIN3
SRP1
RP021
RPC40
RPO26
Gcr2 (4/11)
Tye7 (3/6)
Reb1 (3/19)
TAP186(2/5)
TAP145(3/19)
TAP159(5/50)
TAP62(5/13)TAP229(3/11)
TAP86(5/19)
TAP88(2/9)
c
HXT7
Swi1 (4/5)
HMS286 (2/38)HXT6
PHO84
PRB1
Snf2 (4/6)
HMS184 (2/18)
HMS286 (3/38)
HMS303 (2/3)
HMS98 (2/6)
HMS106 (2/8)
HMS29 (2/18)
Snf3 (1/1)
a
TAP105(20)Abf1(282)6
TAP111(73)
11
TAP115(29)
Dot6(9)
2
TAP133(2)
Hap4(69) 2
TAP144(4)
Hap2(19)
2
Hap3(23) 2 4
TAP146(35)
7
TAP15(3)
Hsf1(55)
2
TAP154(29)
7
TAP155(26)
Thi2(7)
2
TAP156(84)
15
TAP161(82) 3
TAP212(6)Rfx1(32)
2
TAP99(34)
7
HMS100(44)
Hir2(21)
3
HMS117(8)
Mac1(37)2
HMS150(14)
Hir1(30)3
3
HMS172(5)
22
HMS175(10)
2
HMS19(10)
Mbp1(112)
4
HMS200(3)
Pho4(62)
2
HMS250(4)Dig1(38)
2 2
2
Ste12(57)
2
HMS251(14)
3
3
HMS273(50)4
3
HMS28(2)
Rgt1(2)
1
HMS301(12)
3
HMS326(33)7
HMS349(8)
2
2
HMS360(4)
3
HMS397(10)
4
HMS424(5)
2
2
HMS461(5)
Rox1(32)
2
HMS468(10)
Fkh2(108)
3
HMS483(17)
3
HMS55(27)
3
HMS84(47)
Ino4(19)
3
b
a
c
Figure S4: Network graph built using statistically significant (E-value<0.1) overlaps betweencomplexes and the high throughput regulons identified by the genome-wide location analysis(Lee, et al., 2002). Notations are identical to Figure S1. a, b, c are detailed in figure S4.
ATP3
ATP5ATP7
COX4
COX5A
COX6
COX9
TAP133 (2/2)
TAP144 (4/4)
Hap2 (2/19)
Hap3 (3/23)
Hap4 (9/69) QCR2
COR1
HMS483 (3/17)
a
HHF1HHT1
HTA1
HTB1
NOC3
SUI2
Hir1 (6/21)
Hir2 (4/21)
HMS100 (3/44)
HMS150 (3/14)
HMS172 (2/5)
HMS251 (3/14)
HMS424(2/5)
HMS175(2/10)
HMS250 (2/4)
HMS273(4/50)
HMS349 (2/8)HMS55 (2/27)
TEC1
STE12 Ste12 (2/57)
Dig1 (2/38)
b
GCN1
TAP111 (11/73)
TAP105 (6/20)
NOP58
LTV1
ARP9
RRP12
YOR145C
YOR056C
SWI3
PTA1
REF2RNA14 SEC21
TIF1
YGR128C
YLR222CSOF1
YMR093W
TAP146 (7/35)
DHH1
FBA1
RET1
RPB10
RPC25
RPO26RPO31
TAP154 (7/29)
BRX1NOC2RRP7PNO1
TAP156 (15/84)
CCT8RPN10
RPN8
RPT5
YKT6URA7
TAP99 (7/34)
YLL034C
ECM33
IDH1MKT1
PMA2
HMS326 (7/33)
EBP2MSS116
HMS397 (4/10)
Abf1 (64/282)
c
Figure S5 : Detailed view of the genes linking clusters of protein complexes and high-throughputregulons. Each ellipse represents a high-throughput complex, which is denoted as detailed in the main manuscript. Regulons are surrounded by rectangles, and their intersections with complexes are displayed by rounded boxes.a) The 9 common genes are involved in respiration. COX4,COX5A,COX6 and COX9 code for components of cytochrome-c oxydase complex IV ; ATP3,ATP5,ATP7 for the F1F0-ATPase complex , and QCR2 and COR1 for ubiquinol--cytochrome-c reductase complex III. b) The Cluster involving Hir1 and Hir2 transcription factors shows 4/8 genes ,which code for histones, and 3 other genes that are involved in transcription and replication. c) The Big Abf1 regulons is significantly linked with 8 protein complexes. Numerous genes involved in this regulon are of unknown functions or show different functional annotations but a significant part of them are involved in rRNA or tRNA synthesis and processing (13/41).
TAP106 (14)
TAP148 (27)
TAP151 (17)
TAP157 (26)
HMS223 (13)
TAP111 (36)
TAP132 (33)
TAP146 (20)
TAP156 (44)
HMS373 (28)
HMS65 (15)
TAP126 (10)
HMS126 (7)
HMS161 (14)
HMS220 (14)
TAP163 (54)
HMS100 (20)
HMS136 (16)
HMS197 (9)
HMS218 (7)
HMS225 (10)
HMS273 (22)
HMS310 (12)
HMS372 (14)
HMS89 (15)TAP142 (9)
TAP77 (5)
HMS169 (8)
HMS396 (8)
HMS397 (7)
TAP4 (5)
HMS204 (4)
HMS104 (6)
HMS239 (10)
HMS150 (8)
HMS349 (3)
HMS162 (5)
HMS304 (3)
HMS25 (10)
HMS301 (7)
HMS358 (3)
HMS423 (4)
11
8
12
8
10
11
30
8
11
6
6 3 5
6
10
23
79
5
4
5
11
5
6
18
10
5
186
9
25
6
12
139
10
10
10
13
6
12
13
10
10
13
7
5
11
15
5
13
2 3
5
3 7
7
3
36
7
48
4
10
5
3
13
2
34 3
8
44
5
35
4
5
3
5
12
6
7
9
5
5
7
3
3
45 7
2
3
4
5
4
Figure S6: Network linking putative co-regulated genes in different high-throughput multiprotein complexes.Each node represents a group of putative co-regulated genes predicted for a given protein complex,using the combined approach of pattern discovery and discriminant analysis (see main manuscript).The complexes are denoted as in the main manuscript. The number of co-regulated genes in each complexis given in parentheses. The number of co-regulated genes that are in common between two complexes isdisplayed along the line (arc) joining the complexes.The network has two large clusters and a few small pair wise connections. The smaller of the large clusters (framed) corresponds to the complexes pertaining to the proteasome,as detailed in Fig. 7 of the main manuscript.