Results

Experiment 1

Complexes: CORUM [1] - Human complexes are extracted from this database. - 429 net complexes, i.e with proteins in the given network and of sizes greater than 2.

Protein-Protein Interaction Network (PPIN): Human network hu.MAP [2] using all non-zero interactions -

• Variant 1: Full network - 7778 nodes, 56712 edges.
• Variant 2: The full network is reduced to a PPIN containing only proteins present in the complexes for efficiency of evaluation. - 1466 nodes, 8214 edges.

Experiment 2

Complexes: MIPS [3], TAP-MS [4] - 268 net complexes

PPIN: DIP [5] - 4933 nodes, 22274 edges

In this experiment, there are 2 variants in accordance with other methods in literature:

• Variant 1: MIPS as train data, TAP-MS as test data
• Variant 2: TAP-MS as train data, MIPS as test data

Experiment 3

Complexes: MIPS, TAP-MS, SGD [6] - 232 net complexes.

PPIN: CombinedYeast - 6136 nodes, 77051 edges

Constructed by the union of the PPINs: DIP, Gavin, Krogan core and extended [7], Collins [8] and BioGRID [9].

*All yeast data was taken from the website ClusterEPs. The preprocessing steps are outlined in the ClusterEPs paper.

References

[1] Giurgiu, M., Reinhard, J., Brauner, B., Dunger-Kaltenbach, I., Fobo, G., Frishman, G., Montrone, C., and Ruepp, A. (2018). CORUM: the comprehensive resource of mammalian protein complexes—2019. Nucleic Acids Research.

[2] Drew, K., Lee, C., Huizar, R. L., Tu, F., Borgeson, B., McWhite, C. D., Ma, Y., Wallingford, J. B., and Marcotte, E. M. (2017). Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Molecular systems biology, 13(6):932.

[3] Mewes, H. W., Amid, C., Arnold, R., Frishman, D., Güldener, U., Mannhaupt, G., ... & Warfsmann, J. (2004). MIPS: analysis and annotation of proteins from whole genomes. Nucleic acids research, 32(suppl_1), D41-D44.

[4] Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., ... & Edelmann, A. (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature, 440(7084), 631.

[5] Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M., & Eisenberg, D. (2002). DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic acids research, 30(1), 303-305.

[6] Hong, E. L., Balakrishnan, R., Dong, Q., Christie, K. R., Park, J., Binkley, G., ... & Hirschman, J. E. (2007). Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic acids research, 36(suppl_1), D577-D581.

[7] Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., ... & Punna, T. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440(7084), 637.

[8] Collins, S. R., Kemmeren, P., Zhao, X. C., Greenblatt, J. F., Spencer, F., Holstege, F. C., ... & Krogan, N. J. (2007). Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Molecular & Cellular Proteomics, 6(3), 439-450.

[9] Stark, C., Breitkreutz, B. J., Reguly, T., Boucher, L., Breitkreutz, A., & Tyers, M. (2006). BioGRID: a general repository for interaction datasets. Nucleic acids research, 34(suppl_1), D535-D539.