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We further compared the transcript component between the two cell types.
We found that indeed expression levels and primary transcript length were negatively correlated (e.g. oligo-array DS-I: r = −0.142 n = 14236 P<0.0001) and this was common to almost every transcript component indicating the presence of a generalized effect.
In addition, percent composition of each transcript component of each unigene was calculated.
Using the Trinity transcript component level for gene distinction, the top 20 genes from each tissue sample with the highest FPKM values were selected to show expression levels of the most abundant transcripts.
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To test whether the alteration of the branch point sequence by rs10424178 caused the predicted splicing difference in vitro, we cloned the BABAM1 exon 2 and flanking intronic sequence into two minigene plasmid vectors, each containing an alternate allele of rs10424178, transfected each vector into cells and measured the gel band intensity of the two BABAM1 transcript components (28).
Consistent dependencies of transcripts on RNA quality among a number of experiments imply the presence of transcript specific components of the effect.
Additionally, transcripts encoding components of transcription factors known to be induced by ROS and important in the regulation of cellular stress response and apoptosis were differentially expressed.
The mRNAs that were co-purified in this study demonstrated a remarkable enrichment for transcripts encoding components of a protein-protein interaction network that comprises the actin cytoskeleton.
However, mRNA transcripts for components of the PI-3 kinase enzyme complex, Pik3r3 and Pik3cb, and downstream targets of PI-3 kinase signaling, Mapk8 (Jnk) and Frap1 were up regulated 2.8, 1.9, 1.5, and 1.2-fold, respectively (Figure 2C,Table S3) in Pten deficient medulloblastomas.
> Table 7 shows the distribution of transcripts in components.
These transcripts are components of important physiological processes, signaling/metabolic pathways and regulatory networks.
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