Co-cluster signatures help track where two items have co-clustered. Two rows from the pairs table for the A. thaliana dataset: each row starts with the two item IDs (here: A. thaliana proteins), followed by the number of times these two proteins were co-clustered, followed by a co-cluster signature that tells in which clusterings the two proteins were co-clustered. Clusterings order for this example: A. thaliana, Clauset, CFinder, Louvain, MCL, MCODE.F, MCODE, MINE, SPICi. Proteins AT1G04100 and AT1G51950 co-clustered in 8 clusterings. The two share many specific GO annotations: both are involved in auxin stimulus, localize to the nucleus, and participate in protein binding and sequence-specific DNA binding transcription factor activity. AT1G04100 and AT1G50900 were in the same module just once and shared no GO annotations suggesting that the relationship between these two proteins was of a different nature.
Filippova et al. BMC Bioinformatics 2012 13:276 doi:10.1186/1471-2105-13-276