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As a final test for functional equivalence of retroposed and parental copies we compared sex-biased gene expression (Table 2).
Pooling all αCNSs that are 31 bases or longer, we compared the degree of detectability in Br as a measure of the number of expected orthologous copies; we compared singlets with doublets with triplets.
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To investigate whether there was a copy number effect in our data we compared single copy genes to known multiple copy genes in our control strains to look for differences in the normalised log2 Cy3/Cy5) data.
To assess the influence of msh1 recombination on mitochondrial genome copy number, we compared relative copy number at 11 sites within the mitochondrial genome of the wild type (Col-0) and the msh1 mutant.
P value*: Logistic regression analysis To study biological roles of the E2 DNA copy numbers, we compared mRNA expression levels of both LEPR and LEPROT genes with E2 DNA copy numbers in lymphoblastoid cell lines.
Finally, to show that there is indeed a difference in the level of mutually exclusive patterns exhibited by DNA methylation and copy number, we compared the average path length distance of top-ranked differentially methylated genes to top-ranked amplified/deleted genes, using the TCGA data for which both DNA methylation and Affy SNP data is available.
When a library was shared between two paralogous copies, we directly compared the two ratios.
−, copy number deletion We compared DNA copy number aberration profiles of different gastric cancer TNM-stages and histological subtypes, and found 11 noteworthy regions that displayed differences in copy number changes between PD (n = 10) and MD (n = 11).
To control for any visual bias caused by the copy number heatmap, we compared the number of copy number breakpoints for each sample (See Additional file 3).
To determine the copy number of transgenes, we compared the copy number of peIs303 and peIs304 to low copy genomic insertions produced by MosSCI.
Therefore, we calculated the absolute copy number levels assuming that the most commonly found copy number level is 2. We compared the copy number levels found by CG with an earlier measurement using comparative genomic hybridization (CGH) arrays [ 36].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com