We compared our proposed MNet with other related algorithms: ProMK [25], SW [16], OMG [27], LIG [28], and MSkNN [7]. MSkNN first trains a weighted majority vote [31] classifier (similar to a weighted kNN) on each individual network, and then integrates these classifiers for protein function prediction; it achieves competent performance on the first large-scale community based critical assessment of protein function annotation [2]. The details of the other comparing methods were introduced in the section of Related Work, and their parameter setting is discussed in the Additional File 1.