Transcriptional regulation of protein complexes in yeast

Table 2 Results of the pattern discovery and discriminant analysis for annotated complexes

	Annotated complex	ORFs	Coverage	Max sig	Discovered patterns
Permanent	26S proteasome	36	0.83	15.84	24
	19-22S regulator	18	0.94	8.76	16
	20S proteasome	15	0.87	5.76	13
	Respiration chain complexes
	Cytochrome bc1 complex	9	0.67	1.13	4
	Cytochrome c oxidase	8	0.88	1.51	2
	F0-F1 ATP synthase	15	0.67	4.01	4
	Cytoplasmic ribosomes	138	0.68	19.49	151
	Cytoplasmic ribosomal large subunit	81	0.70	11.67	77
	Cytoplasmic ribosomal small subunit	57	0.79	8.97	63
	Cytoplasmic translation elongation	9	0.78	2.35	10
	Cytoplasmic translation initiation	27	0.19	6.31	5
	eIF3	7	0.43	1.24	2
	Nucleosomal protein complex	8	1.00	4.38	20
	RNA polymerase III	13	0.46	1.52	2
	RNA polymerase II holoenzyme	35	0.11	1.81	2
Transient	Microtubules	32	0.16	1.45	5
	Pyruvate dehydrogenase	5	0.60	1.81	1
	Replication complexes
	Replication complex	19	0.42	1.66	5
	SAGA complex	14	0.50	1	5
	Spindle pole body	32	0.13	2.93	8
	SPB components	16	0.25	3.38	8
	Tim22p complex	5	0.40	1.99	1
Others	Cdc28p complexes	10	0.60	2	5
	H⁺transporting ATPase-vacuolar	15	0.40	2.46	6
	Nuclear splicing complexes-Spliceosome	66	0.06	1.55	5
	Other DNA repair complexes	5	0.40	1.11	4
	Replication complexes	49	0.41	15.64	7
	Replication fork complexes	30	0.57	13.28	12
	Respiration chain complexes	37	0.59	8.49	11
	rRNA processing complexes	18	0.22	1.72	2
	t-SNAREs	10	0.40	1.45	3

Column 2 lists the names of the analyzed complexes. Columns 3 and 4 list, respectively, the number of components in the complex and the coverage of the assignment, defined as the fraction of the components of a given complex that are predicted to be part of a putative regulon. Max sig (column 5) is the highest significance index in patterns detected for this complex, and column 6 lists the number of discovered patterns for the complex. Complexes have been subdivided into three categories - 'permanent', 'transient' or 'others' - as indicated in column 1, and described in Materials and methods. Assemblies such as 'Respiration chain complexes', which contain several groups of complexes and hence do not represent a single physical entity, were classified here in the 'others' category. However, smaller complexes, which are part of this assembly and for which putative regulons were identified, were classified as 'permanent'.

ISSN: 1474-760X