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Kaplan Meier curves as function of categorized expression levels of miR-26a and EZH2 visualize their association with TTP (Fig. 1).
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As a first approximation to categorize expression levels, all chromosomal genes of B. methanolicus MGA3 were divided into four groups according to arbitrarily chosen transcripts abundance thresholds (section "Transcript abundances of B. methanolicus MGA3").
Microarray analysis, followed by clustering to reveal the main patterns of gene expression, [ 23] was used to categorize and compare the expression levels of 40,430 genes in wild and domesticated cotton.
The expression levels of ERa were categorized as follows (normalization against RNA of HKG RPS18) for consecutive quantification: group 0: no ERa standard mRNA detectable; group 1: ERa standard mRNA amount ≤0.81; group 2: ERa standard mRNA amount >0.81, due to the mean mRNA level within ERa standard positive samples being 0.81.
The expression levels of transcripts were then categorized into various expression ranges.
The expression levels of the lncRNAs were categorized into high and low levels accordingly.
The expression levels of each gene were categorized as low or high at the 33.3rd, 50th, or 66.7th percentiles.
Reverse engineering approaches have been developed to infer boolean networks underlying changes in the gene expression levels, assuming that expression levels of different genes can be categorized into different states [ 19].
To investigate whether non-conserved genes show lower levels of expression, the expression levels of all conserved and non-conserved genes were categorized according to their RPKM values.
We then evaluated the relative expression levels of E. fischeriana transcripts as described in methods and categorized these into three expression ranges 1-125, 125-250 and more than 250 mean coverage expression level.
The expression levels of the different transcripts that were analyzed in this study are categorized into three categories (Fig. 4).
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