Exact(2)
To assess the biological relevance of the obtained groupings, we calculated the total mutual information between the clustering result and the GO terms assigned to the proteins within the clusters, MI(C,A), according to Steuer et al. [ 25], as in [ 53].
VNTR analyses were included on the construction of the minimum spanning tree method, in order to provide further discrimination between strains for isolates with identical spoligotyping results, Distance matrices are calculated and the obtained groupings can be used to build a dendrogram.
Similar(58)
We obtained some groupings similar to those reported earlier, the V. longisporum lineage A1/D1 corresponded to Zeise and von Tiedemann's [51] group lsp and Clewes et al. 's [26] group alpha.
However, we obtained 17 groupings with the 15 or 20%% missing values.
In an analysis of meningococci across several clonal complexes, Schouls et al. obtained similar groupings by MLVA and MLST (10 ).
We obtained stage grouping data in almost one in two cases.
However, to obtain these groupings, several highly divergent sequences were omitted from the analysis because of their ambiguous placement in the tree.
In order to compare EC with reactome for equivalent number of clusters we obtain the groupings of the reactome with the same number of clusters (6, 39,...).
Therefore we created a "universal" CCS by using the most granular code available for each ICD-9 diagnosis code to obtain 355 groupings in CCS level 4. We separately investigated different levels of ICD-9 granularity by using the first 3- or 4-digit ICD-9 codes [ 16].
However, the gene ontology (GO) groupings obtained for a random sample of 6,536 genes (O. sativa japonica) also showed groupings with statistically significant P values up to P = 1.7 × 10− (supplementary table S2, Supplementary Material online).
We show that this unsupervised clustering results in groups of enzymes more coherent in biological terms than equivalent groupings obtained from the EC hierarchy.
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