Exact(2)
Here again, we assume that any configuration, where each gene is allocated to at least one pathway is valid and that each one is equally likely to occur by chance.
For each individual gene, the program computes a density-based silhouette (dbs) (using the "pdfCluster" package in R), which is a statistical measure of confidence that a certain data point (gene) is allocated to a cluster (here the atypical region) [ 57].
Similar(58)
This combined nuclear and mitochondrial gene dataset was analyzed in MrBayes similar to the larger mitochondrial dataset above with partition-specific models for all codon positions of each protein-coding gene being allocated an independent model according to AIC criteria.
A total of 50 genes were allocated to each cluster.
Distinct distribution into clusters was observed when the specifically affected genes were allocated.
Cosegregating genes were allocated into "recombination blocks" which were sequentially numbered (Additional file 2, Table S1).
In both AD-iPS neuron experiments the largest number of Alzheimer-related genes was allocated to pons.
In the G. ramondii genome, nearly half of the RGA genes were allocated to 26 Rgrcs (Fig. 3; Additional file 2: Figure S3).
Only 4.7% of genes are allocated to "extracellular region", reflecting the fact that only a fraction of the proteins containing signal peptides are destined for the extracellular space [ 18].
Most of the genes were allocated on the right side of the plot (quadrant b), clearly separated from the other variables, showing positive scores for the PC1 and little influence on the PC2.
Next, this consensus green microglia-enriched profile was compared to the consensus blue primed microglia profile, hub genes were allocated, and five categories were defined (see Methods): "brain tissue derived microglia signature", "mainly brain tissue derived microglia signature", "general microglia", "mainly pure microglia", and "pure microglia".
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