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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.