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All ΔΔCt values correspond approximately to the binary logarithm of the fold change as mentioned in the text.
This fit was measured with an SI, defined as the binary logarithm of the quotient of the number of observed and expected cleavage sites.
Among the different ways to compute differential expression, in this paper, we exploit the (binary) logarithm of the ratio between the absolute expression of the gene in the two tested conditions (log ratio).
For each gene, we then computed the binary logarithm of the mean expression level of the gene (i) in those genomes where the gene has a repeat instability compared to the normal tisssue and (ii) in genomes where the gene does not contain an unstable or orphan repeat.
All DDCt values correspond approximately to the binary logarithm of the fold change, as mentioned in Section 3. Renal rat tissue was homogenized in extraction buffer QProteome Mammalian Protein Preparation Kit (QIAGEN), and the whole proteins were extracted by centrifugation (14,000 rpm) for 10 min at 4°C, as recommended by the supplier.
Next, for each gene in a pathway-specific gene set, we computed the binary logarithm of the mean expression level of the gene in those genomes where the gene's promoter shows repeat instability and compared it to the expression level of the same gene, but in genomes where the gene's promoter does not show repeat instability.
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The significantly up and down regulated genes at the four different time points were screened thoroughly according to the requirements that the binary logarithm of fold change should be no less than 2 for up regulated genes and no more than −2 for down regulated genes and P value no more than 0.05.
The list of these 9 genes with some annotation details and the binary logarithm of fold changes of being regulated can be viewed in supplement archive.
Fold change was calculated as binary logarithm of average normalized peak area ratio between the two groups, where the positive value means that the average mass response of HUPM group is higher than LUPM group.
fFold change (FC) was calculated as binary logarithm of average mass response ratio between two groups, where the positive value means that the average mass response of the metabolite in the former is larger than that in the latter and vice versa.
Binary logarithms are also used in computer science, where the binary system is ubiquitous, in music theory, where a pitch ratio of two (the octave) is ubiquitous and the cent is the binary logarithm (scaled by 1200) of the ratio between two adjacent equally-tempered pitches, and in photography to measure exposure values.
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