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Two sets of targets were evaluated, namely (1) Reef Plan Targets (RPTs) representing currently agreed targets, and (2) the more ambitious Ecologically Relevant Targets (ERTs) designed to halt the decline and improve the condition of the GBR.
We focused on two sets of targets: those that are proposed to be regulated similarly by human and chimpanzee forms of FOXP2 and those that seem to be differentially regulated by either form [24].
Three of the top twenty collapsed GO Biological Processes terms were shared between the two sets of targets (see Figure 5A).
That is, in this experiment we had a common set of miRNAs and two sets of targets predicted by TargetScan and miRBase, respectively.
In the response flexibility task, shifting of focused attention was tested by alternations between two sets of targets (letters or numbers) that were presented simultaneously and randomly, one on the left, the other on the right side of the fixation point.
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From the Ingenuity Pathway Analysis database, we extracted two sets of target genes regulated by each transcription factor of interest.
Two sets of target genes were then subjected to canonical pathway analyses using the IPA (Table S8).
The other two sets of target genes shared a similar result, where 5,400 and 5,331 target genes from the novel miRNAs and V3 group were mapped onto these pathways, respectively (Additional file 19: Table S14; Figure 5).
To test whether there was a significant difference in SNP discovery efficiency between the two methods the number of SNPs detected in the two sets of target genes was examined by use of a 2 × 2 contingency table.
If cut-and-paste were the only transposition mechanism of GC42, then we would expect all GC42-absence positions to have either one single set of target site nucleotides (AG) (presumably never inserted or perfectly cut out) or GC42 fragment with two sets of target site nucleotides (AG) as footprint.
If C is the set of all genes, and A and B are two sets of target genes, the probability that their intersection contains z or more genes (under the null model) can be obtained in the R programming language with a call to the hypergeometric distribution function phyper z-1,m,n,k phyper z-1,m,n,k).
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CEO of Professional Science Editing for Scientists @ prosciediting.com