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Table 4 Top 5 predictions of each type for the first group of 60 "ambiguous" annotated proteins.

From: Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study

Type Protein (ORF) Annotation Prediction UniProt SGD
Correct YBL034C ambiguous spindle pole spindle pole Nucleus. Spindle.
cytoskeleton. kinetochore.
spindle pole body (IDA)
  YDR181C ambiguous; cytoplasm; cytoplasm; Nucleus nuclear chromatin (IDA) nuclear chromosome, telomeric region (IC)
  YGR020C ambiguous; vacuolar membrane vacuolar membrane   fungal-type vacuole membrane (TAS) vacuolar proton-transporting V-type ATPase, V1 domain (TAS)
  YHR119W ambiguous; nucleus nucleus Nucleus (Probable). Chromosome (Probable). Set1C/COMPASS complex (IPI)
  YHR183W ambiguous; cytoplasm cytoplasm Cytoplasm cytoplasm (IDA)
mitochondrion (IDA)
Partial Correct YAL029C ambiguous;
cell periphery; bud neck; cytoplasm;bud
Bud Bud cellular bud (IDA)
cellular bud tip (IDA)
filamentous actin (IDA)
mitochondrion (IDA)
  YBR102C ambiguous;
cell periphery;
bud neck;bud
cytoplasm;
bud
secretory vesicle.
Bud. Bud neck.
cellular bud neck (IDA)
cellular bud tip (IDA)
  YBR130C ambiguous;
cell periphery; cytoplasm;bud
bud   actin cap (TAS)
cellular bud tip (IDA)
cytoplasm (IDA)
  YBR260C ambiguous;
cytoplasm;
bud;bud neck;
cytoplasm Cytoplasm. actin cortical patch (IDA)
cellular bud (IDA)
mating projection tip (IDA)
  YFR016C ambiguous;
cytoplasm;bud
cytoplasm   cellular bud (IDA)
cytoplasm (IDA)
Mismatch YAR019C ambiguous; spindle pole cytoplasm   cellular bud neck (TAS)
spindle pole body (IDA)
  YBL105C ambiguous;
cytoplasm;
bud neck;bud
actin   cytoplasm (IDA)
cytoskeleton (IDA)
nucleus (IDA)
  YDL146W ambiguous;
cell periphery;
cytoplasm;
bud neck;bud
actin Bud.
Cytoplasm
Bud neck
colocalizes with actin cortical patch (IDA)
cellular bud (IDA)
cytoplasm (IDA)
cellular bud neck (IDA)
  YDR309C ambiguous;
cytoplasm;
bud
actin Bud neck (By similarity).
Bud tip (By similarity).
cell cortex (By similarity)
cytoskeleton (By similarity).
actin cap (TAS)
cellular bud tip (IDA)
incipient cellular bud site (IDA)
mating projection tip (IDA)
plasma membrane (IGI)
  YHR158C ambiguous;
cell periphery; bud neck; bud
cytoplasm;
nucleus
  cellular bud neck (IDA)
cellular bud tip (IDA)
mating projection tip (IDA)
cytoplasm (IDA)
  YCL024W ambiguous;
cell periphery; bud neck;bud
  Bud neck cellular bud neck (IDA)
      cellular bud neck septin collar (IDA)
incipient cellular bud site (IDA)
  YDL089W ambiguous;
nuclear periphery
  Membrane nuclear periphery (IDA)
Unknown YDR069C ambiguous;
endosome
  Cytoplasm.
Late endosome membrane;
endosome (IDA)
membrane fraction (IDA)
proteasome complex (IPI)
mitochondrion (IDA)
  YDR507C ambiguous;bud
bud neck;cytoplasm
  Cytoplasm.
Bud neck.
cellular bud neck (IDA)
  YHL019C ambiguous;
late Golgi
  coated pit. AP-1 adaptor complex (IPI)
  1. In this table, "Annotation" denotes the experimentally observed subcellular localizations in Yeast GFP Fusion Localization Database [17]. "UniProt" means the subcellular localization in general annotation (comments) in UniProt Database [25]. "SGD" means the cellular component of GO annotation in SGD database [26]. Each type corresponds to different situation of the match between our prediction and the experiment validation.