Table 1.

Features considered in the prediction of nucleolar association

Features	Data source	Description	Bins
Amino acid frequency	Protein sequences from IPI [27]	PNAC considers the relative proportion of leucine, isoleucine, lysine and serine residues	5 bins for each distinct amino acid considered
Targeting motifs	Phobius [32], TargetP[33], NoD [34]	The predicted presence of signal peptides, transmembrane domains (TMDs), mitochondrial targeting peptides and nucleolar localisation sequences (NoLSs)	9 bins detailed in the Methods
Gene co-expression	GDS596 from the Gene Expression Omnibus [42]	The average Pearson correlation of expression between the query protein and proteins in the nucleolar-cytoplasmic training group using expression profiles from 79 physiologically normal tissues [35]	5 bins
GO	EBI Gene Ontology (GO) annotations [36] for human	Biological process and molecular function Gene Ontology (GO) annotations for the query protein are compared to those of the training set proteins	4 bins
Subcellular localisation of interactors	HPRD [31], Uniprot [30], IntAct [39] and PIPs [37,38] subcellular localisation annotations and/or protein interactions	A nucleolar proximity score is calculated for all the interactors of the query protein	5 bins