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Multiple alignments of each clusters were obtained by the program ClustalX [ 48] and T-coffee [ 49], followed by manual inspection and editing.
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For each patient, membership probabilities for each cluster were computed.
Clusters were assigned by visualization of the corresponding dendrogram, and the percent of responders in each cluster were calculated.
CpG sites in each cluster were contiguously located on the CpG island.
The silhouette values for the genes in each cluster were calculated (see Methods).
Sequence similarities among these Puf proteins in each cluster were analyzed and categorized (Fig. 2B).
To do this, genes in each cluster were annotated with their biological process GO terms.
Eigengenes for each cluster were also calculated.
Two representative genes in each cluster were chosen for validation.
The risk estimates for each cluster were identified.
Individual nucleotides of each cluster were sequenced base by base.
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