Additional data file 1:

Table S1: annotations and additional information on all the U-net components. Table S2: modular structure of the U-net. Table S3: feedback regulation of the Ub/Ubl pathway. Table S4: ubiquitination/sumoylation and cellular localization. Table S5: Ub/Ubl pathway and transcription factors. Table S6: cell cycle-related proteins modified by Ubls. Table S7: interactions of the Slx5-Slx8 complex in the MI network. Figure S1: clique degrees and sizes in the U-net and random networks. Figure S2: chromatin proteins regulated by Ub and SUMO. Figure S3: properties of ubiquitinated and sumoylated proteins. Figure S4: logo representation of the flanking regions of ubiquitinated lysines. File S1: plain text representation of the U-net. File S2: multiple sequence alignment of the SUS1 domain.

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