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].

Lee et al. BMC Systems Biology 2011 5:126   doi:10.1186/1752-0509-5-126

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