Resolution:
## Figure 2.
Soft clustering method. (a) Standard clustering based on expression only: two sets of orthologs are depicted (color
represents orthology, shape represents species) where orthologs are split between
clusters 1 and 2. For illustrative purposes, only two time points (t and t + 1) are shown. (b) Soft clustering based on expression and orthology: dashed circles denote regions where
orthologs will be co-clustered. Since the purple square has no orthologs in cluster
1, it remains assigned to cluster 2. (c) Effect of number of clusters k and orthology weight W on GO term enrichment. (d) The number of enriched GO terms, variance, and fraction of co-clustered orthologs
for k = 17 as a function of W in comparison to randomized paralogs/orthologs. Randomization was performed as described
in Additional file 1: Randomizing the Orthology Mapping. (e) Since k-means is non-deterministic, to ensure robustness we performed 50 runs of the algorithm
recording the fraction of times each gene pair was co-clustered (including all genes
from all species). This matrix was hierarchically clustered.
Kuo |