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Using Pearson uncentered correlation, tumours from each cohort were assigned to two clusters (i.e., K-means clustering with K=2, 1000 iterations of clustering) with the threshold of occurrence in the same cluster set to 80%.
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Molecules were manually selected utilizing expert knowledge so they can be assigned to six clusters representing the original six combinatorial libraries the compounds were synthesized in.
The expression profiles of the genes encoding for RPs and RBFs have been assigned to six clusters (see Methods).
The upregulated genes were assigned to three clusters, involved in chemotaxis, cell migration and cytoskeleton organization (Table 2).
The 50 top differentially expressed miRNAs were assigned to four clusters which were almost all highly expressed in pluripotent cells.
To determine if there were gene sets with a similar expression profile over time, SOTA analysis was performed and genes were assigned to four clusters.
The 509 rapeseed inbreds of our study were assigned to three clusters (MCLUST) using a principal component analysis (PCA) of 89 SSR markers as described by Buset al. [ 2].
An additional limitation of using a clustering approach is that each voxel is exclusively assigned to one cluster.
In this method, "fuzziness" relates to the fact that a voxel is generally not uniquely assigned to one cluster, but instead, the similarity of the voxel time course to each cluster centroid is determined.
We found clusters that were consistent with previous results based on average activity measurements from Rea et al. [1], but showed a more complex structure, with the bright worms being assigned to one cluster and the dim worms being separated into two clusters with distinct expression patterns.
We randomly selected 11 samples that were assigned to two molecular clusters based on the FF expression data (Cluster 9 (n=5) and Cluster 18 (n=6); Gravendeel et al, 2009).
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