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The more genes considered, the better taxonomic resolution and the less sensitivity to horizontal gene transfer (Oren and Papke 2010).
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Out of them, BbrizTUB was the less stable while BbrizEF1 followed by BbrizUBCE were the more stable genes considering male and female reproductive tissues, spikelets, roots and leaves.
Two or more genes were considered evolving together if the average correlation coefficient between them was higher than 0.50 and considered highly evolving if correlation coefficient was higher than 0.70 (Fraser et al. 2004).
The cutoff defines the stringency of prediction: the higher the weight cutoff, the more genes are considered as being atypical.
Similar patterns of intersection were found when more genes were considered (data not shown), showing increased consistency at high concentrations.
For a given gene signature, a pathway (or category) that had a hypergeometric distribution probability smaller than 0.05 and included two or more genes was considered an over-represented pathway.
With this method, more genes were considered to be significantly up- or downregulated in IXBhab cells than previously reported, but the expression of genes already reported to be upregulated or downregulated followed the same trend [ 32].
A number of fusion transcripts that are encoded by two or more genes previously considered to be separate have been reported, such as the transcript encoded by exons from the Hsa21, DONSON and ATP50 genes (9).
One of the main problems with this approach is that both the number of equations and the number of parameters of the model--and thus the time required to run the optimisation for fitting the model to the data--increase rapidly as more genes are considered.
Genes that are today considered "coral-specific" may actually be more widely distributed; the number of genes considered vertebrate-specific shrinks with the publication of each additional animal whole genome sequence.
This process is repeated until there are no more genes to consider.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com