*4.10. GeneOntology Terms for Assessing Subcellular Localization*

Subcellular localization was represented using GeneOntology [42] terms from the cellular\_component namespace. Terms attached to complexes in MFIB were mapped to a restricted set of terms, called CellLoc GO Slim, used in previous studies [28] to compare localization of protein–protein interactions. Terms in CellLoc GO Slim were split into five categories: extracellular, intracellular, membrane, nucleus, and other, encompassing other membrane-bounded cellular compartments, such as the lysosome, as well as non-membrane-bounded compartments, such as the chromatin. For CellLoc GO terms attached to MSF complexes, see Supplementary Table S8.

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/21/ 5460/s1.

**Author Contributions:** Conceptualization, B.M., I.S.; Methodology, B.M.; Software, B.M., L.D.; Formal Analysis, B.M., L.D., E.F.; Investigation, B.M., I.S.; Resources, B.M., L.D.; Data Curation, B.M.; Writing—Original Draft Preparation, B.M.; Writing—Review & Editing, B.M., L.D., E.F.; Visualization, B.M.; Supervision, B.M., I.S.; Project Administration, B.M., I.S.; Funding Acquisition, B.M., L.D., I.S.

**Funding:** This research was funded by the EMBO|EuropaBio fellowship 7544 (B.M.), the UNKP-17-3 new national excellence program of the ministry of human capacities of Hungary (L.D.), the project no. FIEK\_16-1-2016-0005 financed under the FIEK\_16 funding scheme (National Research, Development and Innovation Fund of Hungary) (I.S.), Hungarian Research and Developments Fund OTKA K115698 (I.S.). Bioinformatic infrastructure was supported by ELIXIR Hungary.

**Acknowledgments:** The authors express gratitude to Zsuzsanna Dosztányi and Zoltán Gáspári for their comments on the project.

**Conflicts of Interest:** The authors declare no conflict of interest.
