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Table 3 Some notable examples of proteins with newly assigned biological functions with our optimization method

From: Global organization of protein complexome in the yeast Saccharomyces cerevisiae

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]
  1. 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 [4655].