Figure 2

Rules for the classification of TF families. Rules for the classification of TFs and other transcriptional regulators depicted as a bipartite graph. Blue squares represent families, TFs are indicated in solid color, other transcription regulators are indicated by shaded squares. Yellow circles represent protein domains from the PFAM database, orange circles represent domains generated in-house. Continuous edges appear when a domain must be present in members of the family. Discontinuous edges indicate that the domain must not appear in members of the family. The profile-HMMs representing the domains Alfin-like and NOZZLE were created based on outputs derived from PSI-BLAST searches at the NCBI protein database; profile-HMMs for the domains CCAAT-Dr1, DNC, G2-like, GRF, HRT, LUFS, NF-YB, NF-YC, STER_AP, trihelix, ULT and VOZ were created from published multiple sequence alignments. All remaining domains were represented by profile-HMMs downloaded from the PFAM database. This figure is accessible via the Plant Transcription Factor Database http://plntfdb.bio.uni-potsdam.de/v1.0/rules.php, and links are provided to the respective TF families and domains.