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Second, by design, Wagner's method can detect at most one variation cluster per gene.
We will refer to this cluster of residues as the phylogenetic variation cluster (PhVC).
From the ASCA analysis we obtained the main patterns of variation: Cluster pattern A indicates a strong change in expression between 6 hpi and 24 hpi, which is then maintained at time 72 hpi.
For instance, the top-scoring motif PfM21.1 (CATANTGG, log10 P Pf = -27.54) obtained from analysis of the Antigenic Variation cluster (GO 0020033) was identified because large swaths of the promoter regions of these antigenic genes were conserved.
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The random effect ei was split into two components, the spatially unstructured extra-Poisson variation (heterogeneity), ui, and the spatially structured extra-Poisson variation (clustering), vi.
We tested the latter possibility by exploiting the fact that in mice, natural intra-specific IL4 variation clusters at the site 1 epitope for IL4Rα binding.
Other approaches are based on network analysis [ 20, 21] and statistical methods such as analysis of variation, clustering and gene set enrichment [ 22- 24].
It would be good to consider in number terms how many PTMs are in the sequence variation clusters, how many are just nearby and how many are differentiated between the two proteins.
The data also reveal nifD substitution rate variation between cluster I and cluster III diazotrophs.
For unequal sized clusters: where cv is the coefficient of variation of cluster sizes.
As a consequence, the proportion of variation between clusters than within clusters increases, which effectively increases the design effect required to correct for cluster sample designs.
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