However, it is not known how generally this coupling among the requirement of genes for genetic, stochastic and environmental robustness applies.
Since DNA-PK is required for IRF3 but not NF-kB activation (as we show), it is evident that some, but not all, DNA-induced genes will be affected, and these are predictable based on the requirement of genes for these different transcription factors.
Our results support the view that there may not be a difference in the requirement of gene products in the early versus later phases of fusion and all fusion molecules might be involved in activating and sustaining the fusion process albeit through different mechanisms early versus later on during myogenesis.
Due to the requirement of gene expression in vivo, some TSSs are occupied through chromatin remodelling, while others are still in NFRs.
That means most pseudo pathways in our permutation design met the requirement of gene expression correlation, although we did not limit the correlation values of genes when generating pseudo pathways.
Given this requirement of gene copy retention, the last common ancestor of P. infestans, P. parasitica, and P. capsici only experienced 281 gene duplications, whereas the Phytophthora ancestor and the today-living lineage P. infestans had 1,651 and 1,353 gene duplications, respectively.
Compared with other state-of-the-art methods in gene function prediction, SW results in a drastic improvement in performance while reducing the computation time requirement of gene function prediction on five example species (yeast, fly, mouse, human and Escherichia coli).
Large-scale mutant phenotyping monitors changes in mutant fitness or other visible traits, and provides direct assessment of the requirements of genes under specific conditions.
At a strict requirement of all genes being correctly assigned (gene count level) only as little as 3 22% of the RefOGs were recovered, while a more relaxed requirement that curated orthologs are not clustered in multiple OGs or with other homologous proteins that are not part of the RefOG (group count level) results in 10 48% correctly predicted RefOGs.
Most importantly, the number of dead cells following Pttg2 depletion was significantly reduced in cells harboring a homozygous deletion of the p53 or p21 gene, indicating the absolute requirement of these genes during shPttg2-induced cell death.
During interphase, chromosomes and nuclear structures are in constant motion; therefore, correct temporal association is needed to meet the requirements of gene expression.
