Table 8 Sample of the 6086 yeast proteins downloaded from [34] and their biological process annotations identified by PPFBM

YKR087C

GO:0006515 (misfolded or incompletely synthesized protein catabolic process); GO:0006508 (proteolysis)

GO:0044257 (cellular protein catabolic process)

YML120C

GO:0006120 (mitochondrial electron transport, NADH to ubiquinone); GO:0001300 (chronological cell aging); GO:0055114 (oxidation-reduction process); GO:0006116 (NADH oxidation)

GO:0042775 (mitochondrial ATP synthesis coupled electron transport); GO:0022904 (respiratory electron transport chain); GO:0045333 (cellular respiration); GO:0022900 (electron transport chain); GO:0044237 (cellular metabolic process); GO:0009987 (cellular process)

YIL156W

GO:0006511 (ubiquitin-dependent protein breakdown); GO:0006508 (peptidolysis)

GO:0044257 (cellular protein breakdown)

YJL207C

GO:0008104 (protein localization); GO:0006810 (transport); GO:0015031 (protein transport); GO:0042147 (retrograde transport, endosome to Golgi)

GO:0051179 (localization); GO:0051641 (cellular localization)

YML074C

GO:0000412 (histone peptidyl-prolyl isomerization); GO:0018208 (peptidyl-proline modification); GO:0006457 (protein folding)

GO:0000413 (protein peptidyl-prolyl isomerization)

YIL115C

GO:0031081 (nuclear pore distribution); GO:0006810 (transport); GO:0015031 (protein transport); GO:0006611 (protein export from nucleus); GO:0006607 (NLS-bearing protein import into nucleus); GO:0051028 (mRNA transport); GO:0016973 (poly(A)+ mRNA export from nucleus); GO:0000055 (ribosomal large subunit export, nucleus); GO:0000056 (ribosomal small subunit export, nucleus)

GO:0051179 (localization); GO:0034613 (cellular protein localization); GO:0008104 (protein localization); GO:0051641 (cellular localization); GO:0034504 (protein localization to nucleus); GO:0006403 (RNA localization); GO:0033750 (ribosome localization); GO:0051640 (organelle localization)

YNL305C

GO:0019722 (calcium-mediated signaling); GO:0006915 (apoptotic process); GO:0030968 (endoplasmic reticulum unfolded response)

GO:0023052 (signaling); GO:0007154 (cell communication)

YFL016C

GO:0006515 (misfolded or incompletely synthesized protein catabolic process); GO:0006457 (protein folding); GO:0006458 ('de novo' protein folding); GO:0042026 (protein refolding); GO:0006950 (response to stress); GO:0009408 (response to heat)

GO:0044257 (cellular protein catabolic process)

YGL001C

GO:0055114 (oxidation-reduction process); GO:0006694 (steroid biosynthetic process); GO:0016126 (sterol biosynthetic process); GO:0006696 (ergosterol biosynthetic process)

GO:0008610 (lipid biosynthetic process)

YJR068W

GO:0006260 (DNA replication); GO:0006298 (mismatch repair); GO:0006272 (leading strand elongation); GO:0007049 (cell cycle); GO:0007062 (sister chromatid cohesion)

GO:0006261 (DNA-dependent DNA replication); GO:0007059 (chromosome segregation); GO:0009987 (cellular process)

YOR201C

GO:0032259 (methylation); GO:0001510 (RNA methylation); GO:0006396 (RNA processing); GO:0000154 (rRNA modification)

GO:0010467 (rRNA modification); GO:0043170 (macromolecule metabolic)

YNL267W

GO:0046854 (phosphatidylinositol phosphorylation); GO:0016310 (phosphorylation); GO:0048015 (phosphatidylinositol-mediated)

GO:0007154 (cell communication); GO:0023052 (signaling)

YPR188C

GO:0007049 (cell cycle); GO:0051301 (cell division); GO:0000916 (actomyosin contractile ring contraction)

GO:0033205 (cell cycle cytokinesis); GO:0000910 (cytokinesis); GO:0022402 (cell cycle process); GO:0009987 (cellular process)

YOR332W

GO:0007035 (vacuolar acidification); GO:0015991 (ATP hydrolysis coupled proton transport); GO:0006810 (transport); GO:0006811 (ion transport); GO:0015992 (proton trans)

GO:0051179 (localization)

YJR042W

GO:0006606 (protein import into nucleus); GO:0000055 (ribosomal large subunit export from nucleus); GO:0051028 (mRNA transport); GO:0006406 (mRNA transport); GO:0006810 (transport); GO:0015031 (protein transport); GO:0031081 (nuclear pore distribution)

GO:0034504 (protein localization to nucleus); GO:0006403 (RNA localization); GO:0033365 (protein localization to organelle); GO:0008104 (protein localization); GO:0051641 (cell. localization); GO:0033036 (macromolecule localization); GO:0051179 (localization); GO:0033750 (ribosome localization)

YNL090W

GO:0007017 (microtubule-based process); GO:0030010 (establishment of cell polarity); GO:0007015 (actin filament organization); GO:0007264 (small GTPase mediated signal transduction)

GO:0007154 (cell communication); GO:0023052 (signaling)

YMR223W

GO:0006511 (ubiquitin-dependent protein catabolic process); GO:0006351 (transcription, DNA-templated); GO:0034729 (histone H3-K methylation); GO:0051568 (histone H3-K4 methylation); GO:0006508 (proteolysis); GO:0016578 (histone deubiquitination)

GO:0044257 (cell protein catabolic process); GO:0043170 (macromolecule metabolic process); GO:0008152 (metabolic proc.); GO:0010467 (gene exp.)

YML085C

GO:0006184 (GTP catabolic process); GO:0007017 (microtubule-based process); GO:0000070 (mitotic sister chromatid segregation); GO:0045143 (homologous chromosome segregation); GO:0030473 (nuclear migration along microtubule)

GO:0051647 (nucleus localization); GO:0000747 (conjugation with cellular fusion); GO:0051640 (organelle localization); GO:0051641 (cellular localization); GO:0000746 (conjugation); GO:0051704 (multi-organism process); GO:0007018 (microtubule-based movement); GO:0022403

YPR187W

GO:0006351 (transcription, DNA-templated); GO:0006360 (transcription from RNA polymerase I promoter); GO:0006366 (transcription from RNA polymerase II promoter); GO:0006383 (transcription from RNA polymerase III promoter); GO:0042797 (tRNA transcription from RNA polymerase III promoter)

GO:0043170 (macromolecule metabolic process); GO:0008152 (metabolic process); GO:0010467 (gene expression)

YGL103W

GO:0006412 (translation); GO:0002181 (cytoplasmic translation); GO:0046677 (response to antibiotic); GO:0046898 (response to cycloheximide)

GO:0010467 (gene expression); GO:0043170 (macromolecule metabolic process); GO:0008152 (metabolic process)

YGR216C

GO:0006506 (GPI anchor biosynthetic process)

GO:0042158 (lipoprotein biosynthetic process)

YER157W

GO:0016236 (macroautophagy); GO:0030242 (peroxisome degradation); GO:0006886 (intracellular protein transport); GO:0006810 (transport); GO:0015031 (protein transport); GO:0032258 (CVT pathway); GO:0006888 (ER Golgi vesicle-mediated transport); GO:0006891 (intra-Golgi vesicle-mediated transport); GO:0000301 (retrograde transport within Golgi)

GO:0008104 (protein localization); GO:0051641 (cellular localization); GO:0033036 (macromolecule localization); O:0051179 (localization); GO:0034613 (cellular protein localization)

YGR247W

GO:0009187 (cyclic nucleotide metabolic process)

GO:0016070 (RNA metabolic process)

YGL243W

GO:0006396 (RNA processing); GO:0006400 (tRNA modification); GO:0008033 (tRNA processing)

GO:0010467 (gene expression); GO:0043170 (macromolecule metabolic process); GO:0008152 (metabolic process)

YMR166C

GO:0055085 (transmembrane transport); GO:0006810 (transport)

GO:0051179 (localization)

YMR178W

GO:0008150 (biological_process); GO:0006777 (Mo-molybdopterin cofactor biosynthetic process)

GO:0044267 (cellular protein metabolic process)

YML077W

GO:0006914 (autophagy); GO:0006810 (transport); GO:0016192 (vesicle-mediated transport); GO:0006888 (ER vesicle- transport)

GO:0051179 (localization); GO:0051641 (cellular localization)

YML073C

GO:0006412 (translation); GO:0002181 (cytoplasmic translation)

GO:0043170 (macromolecule metabolic proc.); GO:0008152 (metabolic proc.)

YOR035C

GO:0007533 (mating type switching); GO:0030036 (actin cytoskeleton organization); GO:0008298 (intracellular mRNA localization)

GO:0030154 (cell differentiation); GO:0032505 (reproduction of a single-celled organism); GO:0000003 (reproduction)

YOR222W

GO:0055085 (transmembrane transport); GO:0006810 (transport); GO:0006839 (mitochondrial transport)

GO:0051179 (localization); GO:0051641 (cellular localization)

YNL135C

GO:0018208 (peptidyl-proline modification); GO:0000413 (protein peptidyl-prolyl isomerization); GO:0006457 (protein folding)

GO:0009092 (homoserine metabolic process)

YGL200C

GO:0006810 (transport); GO:0015031 (protein transport); GO:0016192 (vesicle-mediated transport); GO:0006888 (ER to Golgi vesicle-mediated transport)

GO:0051179 (localization); GO:0051641 (cellular localization)

YGR260W

GO:0055085 (transmembrane transport); GO:0006810 (transport); GO:0015890 (nicotinamide mononucleotide transport)

GO:0051179 (localization)

YPR166C

GO:0006412 (translation); GO:0032543 (mitochondrial translation)

GO:0010467 (gene expression); GO:0043170 (macromolecule metabolic proc.)

YKR019C

GO:0006914 (autophagy); GO:0006629 (lipid metabolic process); GO:0009267 (cellular response to starvation); GO:0000183 (chromatin silencing at rDNA); GO:0048017 (inositol lipid-mediated signaling); GO:0032258 (CVT pathway)

GO:0007154 (cell communication); GO:0023052 (signaling); GO:0034613 (cellular protein localization); GO:0008104 (protein localization); GO:0051641 (cellular localization); GO:0051179 (localization)

YLR348C

GO:0006810 (transport); GO:0006817 (phosphate ion transport)

GO:0051179 (localization)

YLR431C

GO:0006914 (autophagy); GO:0034497 (protein localization to pre-autophagosomal structure); GO:0006810 (transport); GO:0015031 (protein transport); GO:0032258 (CVT pathway)

GO:0034613 (cellular protein localization); GO:0008104 (protein localization); GO:0051179 (localization)

YJL004C

GO:0006810 (transport); GO:0015031 (protein transport); GO:0043001 (Golgi to plasma membrane protein transport); GO:0006895 (Golgi to endosome transport)

GO:0051179 (localization); GO:0034613 (cell protein localization); GO:0008104 (protein localization); GO:0051641 (cell localization)

YFL055W

GO:0055085 (transmembrane transport); GO:0003333 (amino acid transmembrane transport); GO:0006810 (transp)

GO:0051179 (localization)

YPR179C

GO:0006351 (transcription, DNA-templated); GO:0016575 (histone deacetylation); GO:0007059 (chromosome segregation); GO:0010978 (gene silencing involved in chronological cell aging); GO:0031047 (gene silencing by RNA)

GO:0043170 (macromolecule metabolic process); GO:0008152 (metabolic process); GO:0001300 (chronological cell aging); GO:0007568 (aging); GO:0009987 (cellular process)