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Analysis of complex forming versus noncomplex proteins demonstrates that proteins in complexes have higher essentiality than the noncomplex proteins (average essentiality of complex proteins: 0.1665 (±0.0045) (N = 867), noncomplex proteins: 0.1002 (±0.0014) (N = 3,348); Mann–Whitney U test, P = 1.1 × 10−).
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Our candidate genes are lethal upon inhibition in the context of DDR defects, as depicted by their relatively higher essentialities specifically in DDR-deficient cell lines.
In both analyses, we observe significantly higher essentialities for our genes in DDR-deficient cell lines, thereby indicating that knockdown of these genes is more lethal specifically in the context of DDR defects.
In order to identify those metabolic reactions obeying low flux variability and high essentiality we selected two threshold values.
The gene still had a relatively high essentiality score within the adult-definitive lineage (S = 1.96), determined by the other properties contributing to the score estimate.
For this purpose, metabolic targets with a central role in cancer cell growth were identified by two constraints: low flux variability and high enzymatic essentiality for cancer cell growth.
On the other hand, our computational platform suggests that pyruvate dehydrogenase (PDHm) can perform a central role in driving cell proliferation due to its low flux variability and high enzymatic essentiality for metabolism in cancer cell growth, see Figure 4 (A).
With this in mind, 1,000 objective functions (with components selected from a random uniform distribution ranging from 0 to 1 around numerical values estimated for other organisms [22]) were reconstructed, and enzymes with low flux variability and high enzymatic essentiality were identified in each realization.
Recent efforts at manual re-annotation [ 100] and condition-specific high-throughput essentiality studies [ 38, 101] have continued to improve the existing model.
Such a reaction shows high potential for essentiality [ 2, 3].
This is further augmented with high-throughput gene essentiality data (List-A3).
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