Selection of informative clusters from hierarchical cluster tree with gene classes

BMC Bioinformatics

Table 2 Grouping of obtained functional classes

Colour in figures	Functional group (MIPS)	Member clusters from table 1	Functional group (SGD/GO)	Member clusters from additional file 1.
Blue	cytoplasmic ribosome proteins	1, 8, 12, 19, 40	cytoplasmic ribosomes	1, 11, 19, 27, 30
Red	respiration	2	energy (mitochondria)	8, 14, 15
	AA metabolism	4, 5	AA metabolism	7, 9
Red	mitochondria	3, 6, 14, 24, 38, 47	mitochondrial ribosomes	4, 6 22, 41
Blue	rRNA	7,28
Blue			ribosome biogenesis	2, 3, 5
Blue	translation	36	translation	44
Green	nucleosomal complex	9	nucleosome	16
	proteasome	10, 21	proteasome	13, 28, 39
Green	nucleotide metabolism	13, 45	nucleotide metabolism	25
Green	cell differentiation, pher. resp.	15, 16, 26	mating response (shmoo tip)	49
	phosphate metabolism	17	acid phosphatase/vacuole	50
	lipid metabolism	18, 39	phospholipid metabolism	35, 37
			steroid metabolism	12
Green	cell cycle	20	cell cycle	18, 21
Blue	tRNA	22	tRNA ligase	33
Green			nucleus/RNA and nucleotide processing	10
Green	nucleus	23
Red	CH metabolism, energy	11, 27, 29, 33, 50	energy (CH metabolism)	17, 31, 46, 47
	nitrogen and sulfur metabolism	30	sulfur metabolism	20, 34
			nitrogen starvation	36
			vitamin metabolism	38, 42, 48
	unclassified	31	unknown	40
Red	CH. transport	25, 33	CH transport	43
Blue	mRNA processing	34
Red	cation transport and homeostasis	35, 37, 42	kation transport	24, 26, 29, 32
	cytoplasm	41
	AA degradation (/cell wall)	43, 44
	ER	46, 49	ER	23
	cytoskeleton	48

Different functional class groups obtained with both MIPS and SGD classification using the first 50 clusters. Groups are rough approximate categorizations giving an overview of what functional classes were obtained showing the ordinal numbers for the member clusters. The matching groups for MIPS and SGD classifications are shown on the same line and similar groups are placed to near by rows. The first column shows the colour of the clusters in cluster tree visualizations when it is not black. New abbreviation is ER, endoplasmic reticulum. Other abbreviations are explained in the text for table 1. Functional grouping is based mainly on table 4 [see additional file 1].

ISSN: 1471-2105