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Although the T allele was more strongly repressed by SP3 irrespective of methylation status, the differential repression of the two alleles was diminished by methylation.
This differential repression pattern is exactly what we found for INK4-ARF in hESCs and KRAS-positive CRC cells.
However, we note that differential repression makes sense for the HXT genes, where transporters with different affinities need to be expressed at different glucose concentrations.
Some of the genes with strong differential repression (> 5fold; e.g. MAL, KRT1, GDF15, MMP1; identified by SAM) were not found to be included in these pathways.
A more than twofold differential repression was determined for 26 cloned genomic fragments and the results are summarized in Table 4.
Characterization of these features could be easily followed by a novel technique based on differential repression of the green fluorescent protein expression (Chan et al., 2014).
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Thus, for this small fraction of the total genes in the dataset that were studied (that is, only around the 5% that were differentially expressed from the mid-parent), there was differential expression repression in the hybrid with respect to the two parents.
The expansion and diversification of the KLF/SP gene family within the Metazoa may thus reflect the accumulation of differential transcriptional repression strategies associated with the development of extensive repertoires of cell types required to support complex tissues.
We attempted to identify the most salient reversible miRNA alterations with regards to the generation and/or maintenance of the Rasless status by means of Venn diagrams identifying miRs from Table 1 that showed an exactly opposite pattern of differential expression (repression and induction, respectively) between Rasless cells and both the BRAF-rescued and MEK1-rescued proliferating MEFs.
However, the molecular mechanism by which Oct4 mediates differential activation or repression at these loci to either maintain stem cell identity or facilitate the emergence of alternate transcriptional programs required for the realization of lineage remains to be elucidated.
This analysis evaluated the differential induction or repression of gene networks representing biological modules.
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