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We show at least two regions having striking reductions in heterozygosity ratio, to also be enriched for candidate genes under selection.
Specifically, we predicted that transcripts found in one salinity population but not the other would be enriched for candidate osmoregulatory genes and for osmoregulation-related gene ontology terms (GO; http://www.geneontology.org).org
Because the effects of CNAs are mediated by changes in gene expression, the subset of genes exhibiting concordant changes in both DNA copy number and gene expression (e.g. amplified and over-expressed genes) are likely to be enriched for candidate oncogenes and TSGs.
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Our work is complementary to these studies, showing that GWAS loci from diverse cancer studies are enriched for candidate regulatory SNPs and providing a structured procedure for their identification.
Insights from our study, however, point to the latter, because we found that the list of mito-sensitive genes was enriched for candidate genes that are associated with male-specific fitness, but under-represented by genes that have previously been associated with dedicated sexually-antagonistic fitness outcomes.
Applying comparative genomics to a F. oxysporum strain that causes tomato vascular wilt with Fusarium pathogens of cereals (F. graminearum and F. verticillioides) and pea (F. solani) resulted in the identification of LS genomic regions including four entire chromosomes that are enriched for (candidate) effectors [ 26].
Interestingly, genes identified as responsive to sex chromosome complement in mammals were enriched for candidates sensitive to HP1 [ 60].
Interestingly, though, in the study by Elia et al. [ 28] CNVs segregating with ADHD were found to be enriched for ASD candidate genes, while in several of the ASD CNV studies, family members of the ASD patients also carrying the CNV had diagnoses of ADHD [ 57, 98].
We hypothesized that if the predicted genes are useful for guiding drug discovery, the top-ranked candidate genes would be enriched for the disease-associated genes in GWAS and drug target genes.
By definition, these decreased heterozygosity candidate intervals will be enriched for haplotypes carrying the causative haplotype, and other non-causative haplotypes will be simultaneously depleted from the same phenotype pool.
With few exceptions, the candidate mRNAs localized at sites known to be enriched for either microtubule minus or plus ends.
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