family membership, each PANTHER 7 protein sequence was scored against the HMMs from version 6.1 and assigned to the family with the highest HMM score. If the resulting protein family contained over 1000 sequences, we attempted to manually divide it into smaller families to facilitate web browsing. We divided a total of 20 families from PANTHER 6.1, which have dramatically expanded due to numerous gene (or domain) duplication events, such as G protein-coupled receptors (GPCRs), ATP binding cassette (ABC) transporters, protein kinases, cytochrome P450s (CYP), and proteins containing ankyrin repeats, leucine-rich repeats (LRR), zinc finger and homeobox domains. Figure 1 shows the distribution of family sizes in terms of the number of distinct genes (Figure 1A) and the number of distinct genomes (Figure 1B) they contain.
