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We observed that the recent selective forces on genes reflected by Kp/Ku are in most cases concordant with historical selection pressures on genes, as measured by codon bias.
To find essential genes reflected by pimonidazole staining, we selected the five most significant gene sets covering the three phenotypes proliferation, repair and hypoxia response (Table 1), and extracted the 32 genes with a positive correlation to pimonidazole immunoscore (P<0.05; Table 2).
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Apparently, the increased dCK activity was related to an upregulation of the gene, reflected by an increased mRNA and protein content of the cells.
Reactivation of the endogenous CrChlI gene, reflected by the greening of colorless gametophytes, also indicates that CrChlI silencing is reversible and, therefore, epigenetic.
A caveat and limitation is that the predictive value of CAI is directly dependent on the genes used to establish the "reference set" and may have relatively limited value for predicting expression from genes not reflected by the codon bias found in the reference set.
Histoincompatible reactions in this species entail a wide genome expression, with a prominent representation of immune genes, as reflected by an EST library developed from rejecting Botryllus colonies [14].
The integrative approach utilized here where two clinical subtypes (primary vs. metastases) were compared on both genome-wide copy number and expression levels is a productive methodology for identifying metastasis-relevant genes, as reflected by our ability to define a short list of candidates that included MET receptor tyrosinase kinase and BIRC5.
The impact on proliferation-associated genes is reflected by a reduction of Ki-67 positive cells.
The strength and direction of transcriptional regulation that a TF applies on its target genes are reflected by the weight of the TF presented in the Y matrix.
The SMADs play a major role for the expression of TGFβ1-dependent target genes, as reflected by various classes of rules containing SMAD4 and/or SMAD7 (see additional file 8).
Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.
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