Additional file 1:

Supplementary tables S1 and S2 show the fraction and enrichment in the strong negative effect category of genes in unknown complexes and of unknown genes in complexes, respectively. Supplementary figures S1-6 depict the comparison of the fitness of yeast strains upon deletion of genes in complexes and those not in complexes in all five growth conditions, also when excluding essential genes, as well as for the MIPS and Krogan sets of complexes. Supplementary figure S7 shows the correlation between the number of complexes in which a gene is present and the number of potential interactors, while supplementary figure S8 depicts the fitness of yeast strains in all five growth conditions upon deletion of inessential genes present in multiple complexes. Supplementary figure S9 compares strain fitness upon deletion of protein-coding genes and protein abundance, and supplementary figure S10 compares the fitness of yeast strains upon deletion of genes unique to complex cores and genes unique to attachments in all five growth conditions. Finally, supplementary figure S11 illustrates the similarity of the fitness values for the different yeast deletion strains measured in time-course one and two.

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Additional file 2:

This file provides tables containing the expected fitness effects upon deletion of a random component of the given core or set of attachment proteins for all 5979 isoforms across different growth conditions and the expected fitness effects upon deletion of a random component of whole isoforms, which are visualized in Fig. 5 and Fig. 6, respectively.

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Additional file 3:

This file provides tables containing the set of 491 complexes and the set of 5979 complex isoforms defined by Gavin et al. [9], as well as the set of 266 hand-curated yeast complexes in the MIPS database [29] and the set of 547 yeast complexes defined by Krogan et al. [10]. This file also provides the quantitative fitness data for 4218 non-dubious inessential genes across two fermentable and three non-fermentable media, measured by Steinmetz et al. [3], the confident list of 956 non-dubious essential genes used in this work and the protein abundances determined by Ghaemmaghami et al. [30].

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