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However, if for instance TF1 binds only specifically but TF2 has substantial non-specific binding, TF2 can form as much as two times more complexes than TF1, which should perturb their balance (Figure 5).
CE detects more complexes than SCAN and SCE; LUO detects only 6 complexes for this network.
We then determined which of these pairs occurred in more complexes than expected by chance.
On the other hand, it has recently been observed for a set of 390 protein complexes in yeast, that essential genes are absent in significantly more complexes than expected [ 19].
It is noticeable that the physical interactions identified by BINM, MST and eMST can sufficiently connect more complexes than those identified by AP-MS at a same rank cutoff.
In contrast, for genes that reduce fitness when they are over-expressed, only two bins contain more complexes than expected by chance – one complex has 80 90% of tested subunits with an over-expression phenotype (compared to 0.01 expected, p = 0.006) and 5 complexes have >90% of tested subunits with an over-expression phenotype (1.54 expected, p = 0.02).
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