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We have validated the model predictions regarding a decrease in the initial expression level of EGFR and Cbl family proteins c-Cbl and Cbl-b—in Y992F cells (Figure 6A).
We assessed genes identified in the initial expression profiling experiment to be either regulated more than 2-fold by UAG treatment, or those linked with UAG-regulated pathways identified by GSEA, particularly lipid and carbohydrate metabolism, and adipogenesis.
Though there is increasing evidence that epigenetic changes may play important roles in the initial expression divergence between duplicate genes [ 11- 15], little study has been done about how regulatory network between duplicate genes evolve at epigenetic level.
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In Drosophila, the initial expression of homeotic genes is determined by segmentation genes [ 16] and subsequently this expression pattern is maintained by PcG and trxG proteins [ 17].
Here, each Entrez Gene identifier was mapped to its corresponding object in the Ingenuity Pathways Knowledge Base (IPKB), which resulted in conversion of the initial expression profile into a shorter dataset of well-characterised, non-redundant "focus" genes.
As shown in figure 8, the initial expression domain of toy at the cellular blastoderm stage is cooperatively regulated by the three maternal patterning systems (the anterior, terminal, and dorsoventral systems) cooperatively with the zygotically active gap genes.
Also, in some cases the initial expression of ER + can change to ER- and negatively impact on the long-term course of the disease due to loss of sensitivity to the hormonal treatment [ 26].
In the transcription intervention, the initial expression of each gene was altered to its opposite direction (i.e. from initial up-regulation to down-regulation, or from down- to up-regulation) or to keep the direction the same.
We also found that BeMADS4 and BeMADS2 showed similar expression patterns to wheat orthologs TaPI- 1 and TaPI- 2, including the initial expression in spike primordia and later expression in developing caryopses (5 days after anthesis), lodicules, stamens, and pistils from fully emerged spikes [ 40].
Each time series experiment consisted in strongly increasing or decreasing the initial expression of about one-third of the genes, thereby simulating a physical or chemical perturbation.
In Psg-avrB infected tissues, the initial expression burst (2 hr) was followed by slight decreases from 4 to 12 hr after which a second increase in transcript accumulation was observed at 24, 36 and 53 hrs.
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