Transcriptional regulation of protein complexes within and across species

Tan et al. 10.1073/pnas.0606914104.

Supporting Information

Files in this Data Supplement:

SI Table 3
SI Figure 5
SI Table 4
SI Materials and Methods
SI Table 5
SI Table 6
SI Table 7
SI Table 8

SI Figure 5

Fig. 5. A global view of cellular machinery and its regulation in yeast. Shown are coregulated clusters (squares) identified using yeast only data (green border) or yeast-fly combined data (purple border). Transcription factors regulating the same clusters are merged into a single TF node (octagons). For clearer graphical representation, clusters with >50% overlap (intersection/union of protein sets) are also merged. Numbers of transcriptional interactions are indicated by the thickness of the arrows. Enriched GO biological processes are color coded. Enriched GO cellular components are indicated by text.

Table 3. MIPS complexes significantly enriched for transcriptional interactions

MIPS Complex	Enriched TF
20S proteasome	Rpn4
19/22S regulator	Rpn4
Cytochrome bc1 complex (Ubiquinol-cytochrome c reductase complex, complex III)	Hap4
Cytochrome c oxidase (complex IV)	Hap4
F0/F1 ATP synthase (complex V)	Hap4
Sister chromatid cohesion complex	Mbp1
cytoplasmic ribosomal large subunit	Fhl1
cytoplasmic ribosomal small subunit	Fhl1
Met4 complexes	Cbf1

Table 4. Overview of the predicted protein clusters

	Species	Total complexes	Total proteins	Proteins / complex*	Complexes / protein*	Total TFs	TFs / complex*	Complexes / TF*
Protein Cmplxs	Yeast	452	1789	13.0 (3.4)	3.3 (4.0)
Regulated complexes	Yeast	72	413	10.0 (4.5)	1.8 (1.7)	38	1.7(1.2)	3.3 (3.6)
	Yeast: Conserved Fly:	24	117	10.7 (3.7)	2.2 (2.1)	16	1.8 (1.0)	2.8 (2.0)
	Yeast: Conserved Fly:	24	106	10.3 (4.1)	2.3 (2.2)

* Averages with standard deviations in parentheses.

Table 5. Predicted transcriptional interactions in yeast

TF	Target	Classifier Score^†	Harbison p value^‡	Harbison condition"	Binding site score^§	Complex membership*
Abf1	Snt1	0.934	0.0576	ABF1_YPD	0.77	CA.28
Abf1	Rpo21	0.810	0.7624	ABF1_YPD	0.68	CA.48
Abf1	Cft1	0.973	0.0263	ABF1_YPD	0.83	CA.0
Abf1	Prp3	0.755	0.5725	ABF1_YPD	0.62	CA.70 CB.17
Abf1	Glo3	0.916	0.0528	ABF1_YPD	0.74	CA.12
Abf1	Nup49	0.945	0.0030	ABF1_YPD	0.80	CA.33 CA.52
Abf1	Nop7	0.632	0.0147	ABF1_YPD	0.63	CA.14 CA.51
Abf1	Cic1	0.753	0.5535	ABF1_YPD	0.66	CA.14 CA.51 CA.67
Abf1	Ssf1	0.655	0.0054	ABF1_YPD	0.63	CA.13 CA.14 CA.51 CA.67
Abf1	Bet1	0.923	0.0042	ABF1_YPD	0.76	CA.12
Abf1	Nup120	0.664	0.4867	ABF1_YPD	0.59	CA.33 CA.52
Abf1	Kap95	0.884	0.0015	ABF1_YPD	0.73	CA.33 CA.53
Abf1	Erb1	0.740	0.7329	ABF1_YPD	0.61	CA.13 CA.14 CA.51 CA.67
Abf1	Nop15	0.762	0.4842	ABF1_YPD	0.63	CA.51 CA.67
Abf1	Las17	0.925	0.7701	ABF1_YPD	0.77	CA.2
Abf1	Ret1	0.728	0.0012	ABF1_YPD	0.59	CA.64
Abf1	Rpb10	0.823	0.0126	ABF1_YPD	0.71	CA.48
Abf1	Myo2	0.852	0.3672	ABF1_YPD	0.69	CB.15
Abf1	Rpa190	0.653	0.6034	ABF1_YPD	0.60	CA.48 CA.64
Abf1	Rbd2	0.625	0.6384	ABF1_YPD	0.61	CA.2
Abf1	Rpc40	0.986	0.0780	ABF1_YPD	0.90	CA.48 CA.64
Abf1	Rpc82	0.816	0.0014	ABF1_YPD	0.70	CA.48 CA.64
Cin5	Atp14	0.941	0.0404	CIN5_H2O2Hi	0.94	CA.47
Dig1	Hcm1	0.850	0.0724	DIG1_BUT90	1.00	CB.13
Dig1	Dig2	0.871	0.3476	DIG1_BUT90	1.00	CA.38
Dig1	Gin4	0.650	0.0434	DIG1_YPD	0.79	CB.13
Dig1	Mpt5	0.899	0.0654	DIG1_YPD	1.00	CA.36
Dig1	Dig1	0.938	0.0033	DIG1_BUT90	1.00	CA.38
Fkh1	Mcm2	0.752	0.4447	FKH1_YPD	0.77	CA.8
Fkh1	Cop1	0.816	0.0927	FKH1_YPD	0.79	CA.40
Fkh1	Dhh1	0.655	0.9050	FKH1_YPD	0.68	CA.8 CA.9
Fkh1	Arf1	0.889	0.1205	FKH1_YPD	0.93	CA.40
Fkh1	Sec26	0.900	0.0604	FKH1_YPD	0.93	CA.40
Fkh1	Sec27	0.741	0.6467	FKH1_YPD	0.84	CA.40
Fkh1	Bet1	0.778	0.3098	FKH1_YPD	0.79	CA.40
Fkh1	Sec22	0.908	0.2152	FKH1_YPD	0.93	CA.40
Fkh1	Sec21	0.637	0.3876	FKH1_YPD	0.71	CA.40
Fkh2	Cks1	0.623	0.0020	FKH2_YPD	0.57	CB.18
Fkh2	Cdc28	0.641	0.3078	FKH2_YPD	0.56	CB.23
Fkh2	Htb1	0.923	0.1037	FKH2_H2O2Hi	0.68	CA.16
Fkh2	Hta1	0.930	0.1037	FKH2_H2O2Hi	0.68	CA.16
Fkh2	Snf1	0.915	0.6470	FKH2_H2O2Hi	0.73	CB.18
Fkh2	Vmr1	0.893	0.1033	FKH2_H2O2Hi	0.64	CB.23
Fkh2	Arp4	0.979	0.0664	FKH2_H2O2Hi	0.83	CA.16
Fkh2	Asf1	0.830	0.6028	FKH2_H2O2Hi	0.62	CB.2
Fkh2	Ssn8	0.726	0.0113	FKH2_YPD	0.63	CB.18
Fkh2	Rfa2	0.898	0.1397	FKH2_YPD	0.74	CB.18
Fkh2	Ssn3	0.878	0.5497	FKH2_YPD	0.69	CB.18
Fkh2	Rad53	0.956	0.1458	FKH2_YPD	0.75	CB.2 CB.10 CB.18
Fkh2	Ipl1	0.991	0.0737	FKH2_H2O2Hi	0.90	CB.10
Fkh2	Clb5	0.874	0.2183	FKH2_H2O2Hi	0.64	CB.18
Gal80	Gal80	0.962	0.2498	GAL80_YPD	0.96	CA.56
Gcn4	Smc1	0.888	0.2235	GCN4_RAPA	1.00	CA.59
Hap3	Cox5a	0.652	0.1636	HAP3_YPD	1.00	CA.10
Hap4	Atp4	0.902	0.1694	HAP4_H2O2Lo	0.93	CA.3
Hap5	Cox5a	0.646	0.2164	HAP5_SM	1.00	CA.10
Hsf1	Cns1	0.668	0.0314	HSF1_YPD	0.69	CB.1
Hsf1	Mcd1	0.625	0.3265	HSF1_YPD	0.58	CA.43
Hsf1	Nus1	0.779	0.0134	HSF1_YPD	0.71	CA.53
Hsf1	Gcn2	0.960	0.0782	HSF1_H2O2Lo	0.82	CB.1
Hsf1	Smc1	0.843	0.1028	HSF1_YPD	0.70	CA.43
Hsf1	Kss1	0.780	0.1449	HSF1_HEAT	0.73	CB.12
Hsf1	Irr1	0.738	0.2483	HSF1_YPD	0.70	CA.43
Hsf1	Ssa2	0.990	0.1370	HSF1_YPD	0.99	CB.1
Hsf1	Cdc25	0.777	0.0292	HSF1_YPD	0.71	CB.1 CB.12
Hsf1	Cdc5	0.791	0.2716	HSF1_YPD	0.77	CA.43
Hsf1	Gsp2	0.890	0.5497	HSF1_H2O2Lo