Table 3.

Some notable examples of proteins with newly assigned biological functions with our optimization method

Protein	Known function	Predicted function	Reference
Eno2	Metabolism	Cell division	[46]
Pgk1	Metabolism	Cell division	[47]
Reg1	Metabolism/regulation/cell growth/morphogenesis	Cell division	[48]
Act1	Cell cycle/growth	Mitochondrial biogenesis	[49]
Gsg1	ER to Golgi transport	Cell wall biogenesis	[50]
Ydl203c	Metabolism	Cell wall biogenesis	[46]
Ymr237w	Metabolism	Cell wall biogenesis	[46]
Pep3	Protein targeting, sorting and translocations, vacuolar/lysosomal transport	Cell wall biogenesis	[51]
Ubp15	Cytoplasmic and nuclear protein degradation	Cell wall biogenesis	[52]
Atg17	Cytoskeletal biogenesis	Peroxisome biogenesis	[53]
Gpi8	Lipid, protein modification	Endoplasmic reticulum biogenesis	[54]
Yol070c	Unknown	Bud/growth tip, cell cycle checkpoint	[29]
Hda2	Transcriptional control	Metabolic enzyme	[55]
Iwr1	Meiosis	Transcriptional control	[29]

Reference [29] refers to the case that the predicted functions are not given by the MIPS data [28] so that the functions are not assigned initially, but found by our method and on the Gene Ontology (GO) database [29]. In this case, we consider GO database as the validation source, similar to other references [46-55].