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We removed clusters and terms under each annotation cluster that had P-values larger than 0.05; Table S13 lists 42 enriched clusters with significant P-values.
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We removed clusters with fewer than three proteins.
We removed clusters containing less than 3 members from further analysis.
We removed clusters composed of less than 10 ESTs, leading to a set of 3,599 UniGene clusters.
First, vectors of the removed cluster are re-partitioned to their nearby clusters.
The time complexity depends on the size of the removed cluster.
In step 2, a new partition is found for every vector in the removed cluster.
The MCL-GO clusters for each species were filtered to remove clusters containing only one protein.
Extraction of meaningful subspaces is a procedure to remove clusters that have subspaces corresponding to a non-continuous gene distribution.
We also chose to remove clusters containing only different strains of E. coli (~110 clusters, or 7%), as the high number of closely related strains would cause large and artificially uniform clusters.
In addition, we showed that an inherent property of clustering, the LT, could be used to remove clusters that will probably not be part of the BF partition.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com