For the 'within' permutation, a permuted data sample is created by choosing a new tuple of data (i.e. matched gene expression and gene copy number) first by choosing a random real sample, and then by choosing a random gene from within the same pathway, until tuples have been chosen for each gene in the pathway.
5XFAD mice with BACE1+/+ or BACE1+/− genotype at 6 months of age showed only marginal or no increase in phospho-eIF2α levels consistent with their normal levels of BACE1 that matched the gene copy number.
Of 10,162 matched genes, 5,853 genes (58%) showed a standard deviation >0.5 in mRNA expression, and 2,242 (38%) of these genes showed significant correlation between expression and copy numbers (P < 0.05 adjusted for multiple testing) (Additional file 11).
To ensure a fair comparison between the two models, they must be matched before the gene copying takes place.
In order to assemble each gene copy, matching reads for each reference gene were identified from a database of all trimmed reads from each endophyte genome, through a similarity search using BLAST, defining the E value threshold as 0.1.
This observation is in line with the previous observation [ 13] that this pathway is the least divergent pathway between colorectal tumors and their matched normal genomes in terms of gene copy number variation and gene expression.
Fifteen breast cancer cell lines and 92 primary breast tumors (33 with matched normal tissue) were used to check somatic mutation and gene copy number of PIK3CA.
On the one hand multicopy plasmids may favour fine tuning of the gene copy number to match the required expression levels, on the other hand it may be more difficult to reach a stable phenotype for mixed sugar utilization unless careful selection pressure (such as successive cultivation on alternative sugars) is applied.
However, they are also highly dependent on other factors, such as the efficiency of PCR amplification in relation to, for example, the matching of primers to individual gene copy sequences.
In the influent sample, the percentage of 16S rRNA gene copy and the cell number matched with each other consistently for most of the genera.
