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The background promoter set is sampled 100 times randomly from promoters of all EnsEMBL mouse genes excluding those reported as clock controlled.
A similar result was obtained for the P values derived from the analysis of the gene expression: the absolute Z score was higher among cell adhesion genes (excluding those among the top 1649 genes) than was the average Z score (t test = 1.81, df = 17811, P = 0.07 on the two-tailed test and P = 0.03 on the one-tailed test).
For these comparisons, we selected the common genes excluding those presenting a CV ≥ 30.
Consequently, 43 266 protein-encoding genes excluding those TEs were assigned in the assembled genomic sequences, ∼72% of which showed sequence similarity to registered genes (Supplementary Table S6).
We sequenced 39 annotated genes (excluding those annotated as retrotransposon, transposase, and transposable elements) but did not identify any mutation (Additional file 1).
To generate the control interaction data set, we randomly distributed CLASH targets in the 3′UTR of RefSeq genes (excluding those fragments overlapping with a CDS).
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G represents the set of genes excluding these with Y gk = 0 or Y gr = 0.
(C ) Dot plot showing the Pearson's correlation between RNA-seq and quantitative polymerase chain reaction (qPCR) values for all the annotated genes surveyed (excluding those housekeeping genes used to normalise the data); 43/59 genes show a high concordance between methods (r >0.4).
The substitution rates of most ranoid mt genes (excluding trns) were significantly faster than those of non-ranoids (Nos.
Most of the remaining FESs (57.5% = 1,403/2,439) were related to r-RNA genes; only 590 (2.8%) FESs might contain protein-coding genes after excluding those deriving from mitochondria and transposons.
ESTs were rechecked to represent OR genes by excluding those whose genomic locations overlapped exons of the non-OR subset from the UCSC known gene table [ 68].
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