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In Table 4 and 5, there are ~30% of genes in the co-targets set are essential based on the essentiality information retrieved from TB [ 70] and DEG v5.0 database [ 71].
Bisulfite-sequencing was based on nucleotide sequences in electropherograms.
Based on gene essentiality analysis, the genome-scale metabolic model of B. cenocepacia was further refined.
The sequence logo based on 30 homologous sequences is shown above representative examples from the indicated species.
Our methodological improvements enable unbiased genome-wide clustering based on co-essentiality profiles; we recover pathways and complexes as diverse as MAPK/ERK, PI3K/ACT/mTOR, the ribosome, the peroxisome, regulators of the DNA damage response and chromatin remodeling.
Among these models, the simplest one is prediction of essential genes based on the known essentiality of homologous genes [ 18- 21].
One is based on PPI's essentiality.
Based on the different essentiality of metabolites, the metabolites were classified into three groups: Universal Metabolites (UM): Some inorganic or cofactor metabolites, such as CMP and ATP, which have been found to exist universally in more than 90% organisms.
Comparison to a ranked gene list based on an shRNA essentiality screen in several different cancer cell lines [ 33] shows the significant predictive power of the FASTCORMICS models (Additional file 1: Table S1).
We compared the results of this simulated essentiality screen with experimental gene essentiality results based on both narrow and broad gene essentiality criteria.
Primer sequences for sequencing library construction were based on Sanjana et al.38.
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