Yeast, human, mouse and fly datasets
We evaluate our methodology on benchmark networks of four datasets obtained from the study by [16], which cover four species: yeast, human, mouse, and fly. The Yeast dataset includes 44 functional association networks, the Human dataset includes 8 networks, the Mouse dataset consists of 10 networks, and the Fly dataset has 38 networks. These datasets are publicly available at http://morrislab.med.utoronto.ca/~sara/SW/, and more information about them can be found in [16].
We annotated the proteins in each dataset using the recently updated GO term annotation (access date: 2014-05-13) in three sub-ontologies, namely biological process (BP) functions, molecular functions (MF), and cellular component (CC) functions, respectively. Each protein is also annotated with its ancestral function labels. As suggested by Pandey et al. [19], the functional labels which have too few member proteins are not likely to be testable in the wet lab, and thus of no interest to biologists. We retained the function labels which have at least 10 member proteins. In addition, we removed the functional labels that have more than 300 member proteins: these functional labels are too general and their prediction is not as critical as for the others [25,39]. The statistic of these datasets is given in Table 1. In the table, the BP labels are the biological process functions (or terms), the MF labels are the molecular functions, and the CC labels are the cellular component functions in the Gene Ontology.
Table 1  Dataset statistics.
Dataset  #Proteins  #Networks  #BPs  #MFs  #CCs
Yeast  3904  44  1089  307  224
Human  13281  8  3413  681  438
Mouse  21603  10  4123  818  511
Fly  13562  38  1883  481  315
'#Proteins' represents the number of proteins in a dataset, '#Networks' means the number of functional association networks, '#BPs' denotes the number of BP labels, '#MFs' denotes the number of MF labels, and '#CCs' denotes the number of CC labels.