Sentence examples for most variable CpG from inspiring English sources

Using two-way hierarchical cluster analysis, the most variable CpG sites for each gene were clustered based on pair-wise Euclidean distances and linkage algorithm for all studied samples according to the previously developed method by Gene Expression Statistical System (GESS) version 7.1.19 (NCSS, Kaysville, Utah, USA) [16], [17], [18].

From these, the most variable CpG sites were used for cluster analyses.

The 5000 most variable CpG sites in the dataset were used as input for this analysis.

Hierarchal clustering was based on Manhattan distance and average linkage of the 10,000 most variable CpG loci.

The tree plot of mean-centered β-scores of these top 200 most variable CpG sites is provided in Additional file 2: Figure S2.

After that, we calculated the average DNA methylation level of the 5000 most variable CpG sites in T2E-positive and T2E-negative PCa, stratified by genetic location.

Next, we performed multidimensional scaling of the top 1% most variable CpGs to assess the inter-sample variability within each dataset.

Consensus clustering of 40 samples and 10,000 most variable CpGs identified 2 clusters as the optimal number.

Unsupervised clustering of the 1% most variable CpGs (excluding probes that map to sex chromosomes or with known SNPs at the target site; termed XYS probes) revealed clear separation of samples into tissue-related groups, confirming the significant association between tissue type and methylation.

Additional file 5 is a PCA showing the two discovery study samples on the first three principal components, using only the most variable autosomal CpG sites.

(DOCX 38 kb) Additional file 5: Principal component analysis of the two study groups (n  = 355) on the first three principal components, using only the most variable autosomal CpG sites.