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The complete probe set used for microarray analysis contained all annotated genes for nitrogen metabolism for each included genome, and in many cases, genes from both nitrate assimilation and dissimilatory nitrate/nitrite reduction pathways were present in the same organism.
The resulting groupings suggest the existence and operation of common regulatory influences or a requirement for co-expression as, in many cases, genes with similar or related functions are present in the same group.
In many cases, genes exist in several copies (Hat et al. 2007) (and references therein).
In many cases, genes highly ranked for differential abundance between treatments corresponded to the activation of particular pathways.
However, in many cases genes that show genetic interactions have phenotypes themselves, and more general methods to predict directionalities have been lacking.
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In many cases, gene identification has enabled significant insight into the physiopathology of the related conditions.
In many cases, "gene trees" and "species trees" may not be equivalent, a fact that complicates (but does not preclude) the reconstruction of phylogenies using molecular information (e.g., Wolf et al. 2002; Rokas 2006).
In many cases, gene expression is primarily regulated via transcription under the control of enhancer and promoter sequences.
In many cases gene activities are correlated, e.g., due to a common upper stream regulator.
In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed.
Hundreds of putative membrane proteins and lipoproteins were predicted, although in many cases, gene annotation may be incomplete or inaccurate to reliably identify putative vaccine candidates.
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