The neighbor-joining method was used to analyze the distance matrix, and dendrograms were generated by using the phylogenetic analysis program PAUP* version 4.0b (22 ).
PCA, correlation matrix and dendrogram also confirmed that there was no significant batch effect between the two Illumina slides in our experiment.
Consensus similarity matrix and dendrogram based upon individual matrices from different markers were used for pair wise clustering based on unweighted pair group method (UPGMA) with average linkages (11).
Cluster analysis was also carried out using the unweighted pair-group method with arithmetic average (UPGMA) based on the Nei's genetic distance matrix and dendrogram was drawn to show the clustering pattern of the different genotypes using NTSYS-pc.
Further network parsing, matrix construction, and dendrogram parsing was done using C /.NET 4.0 on a Windows 7 machine.
We then made profiles for individual subtypes and features, calculated the distance matrices, and constructed a dendrogram for each feature.
Additional file 1: Figure S4 and S5, respectively, depict a heat map of the correlation matrix and a dendrogram depicting an average linkage, one minus absolute correlation distance clustering of the 12 PhyloP variables used to construct the PCs.
The modified Kullback-Leibler distance method was used to create a pairwise percent similarity matrix, and a dendrogram was generated using the unweighted pair group method of arithmetic averages.
Additional file 1: Figure S1 and S2, respectively, depict a heat map of the correlation matrix and a dendrogram depicting an average linkage, one minus absolute correlation distance clustering of the 75 Broad ChIP seq variables used to construct the PCs.
Additional file 1: Figure S7 and S8, respectively, depict a heat map of the correlation matrix and a dendrogram depicting an average linkage, one minus absolute correlation distance clustering of the 24 Caltech RNA seq variables used to construct the PCs.
