Table 2.

Consistently misclassified genes

Class	Gene	Locus	Error	Description
TCA	YPR001W	CIT3	FN	Mitochondrial citrate synthase
	YOR142W	LSC1	FN	α subunit of succinyl-CoA ligase
	YLR174W	IDP2	FN	Isocitrate dehydrogenase
	YIL125W	KGD1	FN	α-ketoglutarate dehydrogenase
	YDR148C	KGD2	FN	Component of α-ketoglutarate dehydrog. complex (mito)
	YBL015W	ACH1	FP	Acetyl CoA hydrolase
Resp	YPR191W	QCR2	FN	Ubiquinol cytochrome-c reductase core protein 2
	YPL271W	ATP15	FN	ATP synthase ɛ subunit
	YPL262W	FUM1	FP	Fumarase
	YML120C	NDI1	FP	Mitochondrial NADH ubiquinone 6 oxidoreductase
	YKL085W	MDH1	FP	Mitochondrial malate dehydrogenase
	YGR207C		FN	Electron-transferring flavoprotein, β chain
	YDL067C	COX9	FN	Subunit VIIa of cytochrome c oxidase
Ribo	YPL037C	EGD1	FP	β subunit of the nascent-polypeptide-associated complex
	YLR406C	RPL31B	FN	Ribosomal protein L31B (L34B) (YL28)
	YLR075W	RPL10	FP	Ribosomal protein L10
	YDL184C	RPL41A	FN	Ribosomal protein L41A (YL41) (L47A)
	YAL003W	EFB1	FP	Translation elongation factor EF-1β
Prot	YHR027C	RPN1	FN	Subunit of 26S proteasome (PA700 subunit)
	YGR270W	YTA7	FN	Member of CDC48/PAS1/SEC18 family of ATPases
	YGR048W	UFD1	FP	Ubiquitin fusion degradation protein
	YDR069C	DOA4	FN	Ubiquitin isopeptidase
	YDL020C	RPN4	FN	Involved in ubiquitin degradation pathway
Hist	YOL012C	HTA3	FN	Histone-related protein
	YKL049C	CSE4	FN	Required for proper kinetochore function

The table lists all 25 genes that are most consistently misclassified by the SVMs. Two types of errors are included: a false positive (FP) occurs when the SVM includes the gene in the given class but the MYGD classification does not; a false negative (FN) occurs when the SVM does not include the gene in the given class but the MYGD classification does.