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However, the reliability of phylogenetic studies based on selected genes may be impaired by a selection bias, in particular due to recombination or lateral gene transfer, as previously described for Rickettsia species [31].
The use of DNA microarrays based on selected genes (and gene variants) that are involved in interesting processes can be used to assess a community's ability to perform a collective function, such as biodegradation of contaminants, and monitor, for example, during bioremediation changes over relevant periods.
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In the high-level analysis, partitioning genes into closely related groups across time and classifying patients into different health statuses based on selected gene signatures have become two main tracks of microarray data analysis in the past decade [2] [6].
So it was concluded that used approaches can satisfactorily predict survival based on selected gene expression measurements.
In the past decade, two main tracks of analyses of microarray data have been to partition genes into closely related groups across time using clustering techniques and to classify patients with different health statuses based on selected gene signatures [ 2- 6].
These p-values are easier to interpret, more meaningful and easier to compare than weighted mean distances: They describe how much better the results taken from the bioinformatics tools are, compared to "pathways" based on selecting genes randomly, and they are not affected by topological bias in the network.
To reduce the likelihood of false-positive results, we used a relatively stringent FDR of 1% and conducted control analyses to determine expected rates of differential gene expression based on either all available genes on the array, or 10 iterations of analyses based on randomly selected genes.
Hierarchical cluster analysis based on these selected genes separated into two branches, one for ND and one for RA patients.
Table 3 presents the classification accuracy comparison using SVM and NB classifier based on the selected genes using these six feature selection methods, when the number of selected gene is 30.
Liver cancer (Livca) shows a distinct gene expression profile with all other cancer types listed based on the selected genes.
Individual trees based on the selected genes also presented a similar phylogenetic portrait of the genus (data not shown).
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