Consistent probabilistic outputs for protein function prediction

Table 1 Summary of data types

Data type	Description	BP	CC	MF
Phenotype
MGI	Mammalian phenotype ontology terms (33)	1,994	2,157	1,898
OMIM	Diseases (2,488) associated with human homologs	998	1,166	978
Phylogenetic profile
Inparanoid	Orthologs across 21 species	6,131	7,092	6,556
Biomart	Orthologs across 18 species	6,269	7,242	6,695
Protein domain
Interpro	Functional sites and domains	7,131	8,027	7,603
PfamA	Protein domains	6,790	7,648	7,239
Protein-protein interaction
PPI	Transferred via orthology from human (OPHID)	3,273	3,690	3,509
Gene expression data
Su et al. [9]	Oligonucleotide arrays (55 tissues)	6,555	7,587	7,029
Zhang et al. [7]	Affymetrix arrays (61 tissues)	5,097	5,716	5,447
SAGE	Tag counts from SAGE library (99% cutoff)	6,323	7,231	6,753
Total		7,968	9,005	8,427

The table lists the ten data types from [1], along with the number of proteins that are annotated with at least one term of each ontology and for which that data type is available. BP, biological process; CC, cellular component; MF, molecular function.

ISSN: 1474-760X