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No associations between the clustering pattern and the clinical features were apparent.
Hierarchical clustering of the samples based on the DNA copy number changes showed no associations between the clustering pattern and the tumour subtype or the other clinical features (Figure 1), and no chromosomal regions with significantly different DNA copy number between the primary tumours and recurrences were found.
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Correlations between the clustering patterns and the ER status or the breast tumour phenotype were investigated using a Pearson χ test.
The full correlation matrix of 77 metabolites versus gene expression is presented at Additional file 3, also showing an overall agreement between the clustering patterns of the main metabolite groups as derived from the metabolite-versus-metabolite analysis.
This clustering pattern displays the distinction between the SU5416 and control arms based on relative expression data, and also indicates further distinctions among subsets of patients as well as the degree of overlap between trial arms in the clustering pattern.
Although smaller groups of MFHs and leiomyosarcomas clustered separately, there were no overall significant differences in the clustering pattern between the two tumour types.
Hierarchical clustering of the samples based on the DNA copy number changes showed no major differences in the clustering pattern between the two tumour types (Figure 4A), similar to what has been reported by others [19], [23].
Looking directly at the correlation matrix of metabolite accumulation versus gene expression, for the large majority of metabolites, the clustering pattern remains constant between the metabolite versus metabolites and metabolites versus gene matrices.
The clustering pattern, although important, remains unexplained.
However, the clustering pattern was more complicated.
The difference in the clustering patterns between all the reads and only the KO-assigned reads was likely ascribable to the biased property of KEGG DB, since this DB was constructed by using mainly the organisms for which complete genome sequences were available.
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CEO of Professional Science Editing for Scientists @ prosciediting.com