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In cases where all reads, or a vast majority of the reads, have identical initial sequences, the image analysis software removes clusters as it considers these to originate from one initial DNA molecule and therefore uninformative.
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We removed clusters with fewer than three proteins.
The MCL-GO clusters for each species were filtered to remove clusters containing only one protein.
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.
Extraction of meaningful subspaces is a procedure to remove clusters that have subspaces corresponding to a non-continuous gene distribution.
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.
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.
The list of detected clusters was filtered by removing clusters that include less than 25 genes or more than 33% of all genes, or have less than 25 intra-cluster interactions.
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.
This score is used to remove clusters with low signal to noise ratio (often caused by clusters being too close to each other so their signals bleed into one another).
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