Classifying pairs with trees for supervised biological network inference

Marie Schrynemackers, Louis Wehenkel, M. Madan Babu, Pierre Geurts


Datasets are provided in the exact form they were used in the paper "Classifying pairs with trees for supervised biological network inference".
Please refer to, and cite, the corresponding publications for the original datasets.


Protein-protein interaction network (PPI)
von Mering, C. et al. (2002) Nature, 417, 399–403.

Protein list
Feature list
Feature matrix
Adjacency matrix

Epistatic Mini-Array Profile (EMAP)
Schuldiner, M., et al. (2005) Cell, 123, 507– 519.
Hillenmeyer, M. et al. (2008) Science, 320, 362–365.

Gene list
Feature list
Feature matrix
Adjacency matrix

Metabolic network (MN)
Yamanishi, Y. and Vert, J.-P. (2005) Bioinformatics, 21, i468–i477.

Gene list
Feature list
Feature matrix
Adjacency matrix

E.coli regulatory network (ERN)
Faith, J. J., et al. (2007b) PLoS Biol, 5(1), e8.

Gene list
Transcription factor list
Feature list
Gene feature matrix
TF feature matrix
Gene-TF interaction matrix

S.cerevisiae regulatory network (SRN)
MacIsaac, K. D., et al. (2006) BMC Bioinformatics.
Hughes, T., et al. (2000) Cell, 102, 109–126.
Hu, Z., et al. (2007) Nature genetics, 39, 683–687.
Chua, G., et al. (2006) PNAS, 103, 12045–12050.
Faith, J., et al. (2007a) Nucleic Acids Research, 36, 866–870.

Gene list
Transcription factor list
Gene feature list
TF feature list
Gene feature matrix
TF feature matrix
Gene-TF interaction matrix

Drug-protein interaction network (DPI)
Yamanishi, Y., et aL. (2011) Journal of Chemical Information and Modeling.

Drug list
Protein list
Chemical substructure list
PFAM domains list
Drug feature matrix
Protein feature matrix
Drug-protein interaction matrix

DPI (enzymes)
Yamanishi, et al. (2008). Bioinformatics, 24(13), i232–i240.

Drug list
Protein list
Drug feature matrix
Protein feature matrix
Drug-protein interaction matrix

DPI (ion channels)

Drug list
Protein list
Drug feature matrix
Protein feature matrix
Drug-protein interaction matrix

DPI (G-protein-coupled receptors)

Drug list
Protein list
Drug feature matrix
Protein feature matrix
Drug-protein interaction matrix

DPI (nuclear receptors)

Drug list
Protein list
Drug feature matrix
Protein feature matrix
Drug-protein interaction matrix