Skip to main content

Table 1 Manually and automatically derived PP-clusters*

From: Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns

Procedure of PP-cluster definition Number of PP-clusters Total number of COGs in all clusters COGs shared with manually derived PP-clusters Average number of COGs in a cluster Number of clusters absent in manually derived PP-clusters Number of pure RS clusters FPs
Manual annotation 223 890 N/A 4.1 N/A - -
Automated tree cutting at average branch length 0.2 89 1,774 315 19.9 38 20 0.19
Automated tree cutting at average branch length 0.3 89 3,960 395 44.5 26 12 0.16
  1. *PP-clusters, clusters of COGs functionally linked on the basis of similar phyletic patterns. RS clusters: clusters containing only COGs annotated as 'poorly characterized' in COGs database, where R stands for 'general function prediction only' and S stands for 'function unknown'. The number of false positives (FPs) is the proportion of clusters that were not presented in manually derived PP-clusters.