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The difference in representation between known open and closed chromatin loci can be reliably detected by the GCSDI assay after treatment with diverse amounts of DNase I, and thus is a reliable analysis outcome that is not overly sensitive to DNase I treatment conditions (Additional file 1: Figure S1).
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A significant difference in representations between the NANOG-binding sites embedded within truncated or full-length L1 sequences and those located either within or outside the LAD boundaries was observed.
Several targets from four of the different HeLa major RNA species (miRNA, tRNA, mRNA, and ncRNA) showed significant differences in representation between the two sample types.
This identification was made through the use of an information theoretic motif-finding method called the Robins-Krasnitz algorithm, described previously[5].The algorithm identifies dozens of motifs that exhibit substantial differences in representation between the HIV-1 genome and the human coding genes.
Genes and transcripts with the largest differences in representation between oil exposure and control libraries were annotated with Blast2GO.
Other differences in representation between Tortula and Physcomitrella mappings relate to a higher representation for Tortula in the categories that relate to responses to external stimuli and responses to stress both of which would seem consistent with the emphasis that cellular activity for Tortula would have in comparison to unstressed Physcomitrella cells.
With respect to domain composition, there was a striking difference in representation of some Pfam domains between the chromosomes, suggesting the presence of genes coding for different suites of proteins on the two chromosomes.
If the difference in proxy representation between the two studies is due to the HRS being more likely to use a proxy for a respondent with impaired cognitive function (whereas the ELSA would still use a self-report interview), this could lead to the pattern of better apparent cognitive performance among the HRS self-respondents compared to the ELSA self-respondents included in our study.
PCoA analysis of Unifrac distances calculated between all samples showing the differences in representation of taxa between the samples.
The proportion of clones in each library assigned a particular GO function were compared between different libraries and chi square used to indicate significance differences in functional representation between libraries (*** p ≤ 0.001, ** p ≤ 0.01,* p ≤ 0.05).
As a control, we examined DNA segments present in the transgene constructs (and thus at higher copy numbers) in the individual lines; this analysis showed the expected substantial differences in tag representation between samples (data not shown).
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