Supplementary Material for

Adryan and Teichmann (2006): Drosophila transcription factor database: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster.

GO terms used for seeding the candidate transcription factor lists

The manuscript describes our strategy to seed a list of candidate transcription factors based on the Gene Ontology annotation that is used in FlyBase. We used two rounds of seeding with two different levels of stringency.

• For the first round ("the text book examples") we sought proteins with GO terms
  transcription factor activity (GO:0003700) OR RNA polymerase II transcription factor activity, enhancer binding (GO:0003705)
  
  or GO term combinations of
  DNA binding (GO:0003677) AND one of
  RNA polymerase I transcription factor activity (GO:0003701) OR RNA polymerase II transcription factor activity (GO:0003702) OR specific RNA polymerase II transcription factor activity (GO:0003704) OR ligand-regulated transcription factor activity (GO:0003706) OR RNA polymerase III transcription factor activity (GO:0003709) OR transcription coactivator activity (GO:0003713) OR transcription corepressor activity (GO:0003714) OR general RNA polymerase II transcription factor activity (GO:0016251) OR transcriptional activator activity (GO:0016563) OR transcriptional repressor activity (GO:0016564) OR general transcriptional repressor activity (GO:0016565) OR specific transcriptional repressor activity (GO:0016566) OR negative regulator of basal transcription activity (GO:0017163) OR transcription regulator activity (GO:0030528)
  
  See the results of this search (498 candidate transcription factors).
  
  
• The GO terms for the second round ("those with some hints") were determined empirically from known transcription factors that were not yet found in the first screen. The second round was seeded exclusivley with proteins which were not yet in the first list, and that were having GO term combinations
  nucleic acid binding (GO:0003676) OR DNA binding (GO:0003677) AND
  nucleus (GO:0005634)
  
  or combinations of
  nucleic acid binding (GO:0003676) OR DNA binding (GO:0003677) OR nucleus (GO:0005634) OR transcription factor complex (GO:0005667) AND one of
  RNA polymerase I transcription factor activity (GO:0003701) OR RNA polymerase II transcription factor activity (GO:0003702) OR specific RNA polymerase II transcription factor activity (GO:0003704) OR ligand-regulated transcription factor activity (GO:0003706) OR RNA polymerase III transcription factor activity (GO:0003709) OR transcription coactivator activity (GO:0003713) OR transcription corepressor activity (GO:0003714) OR transcription, DNA-dependent (GO:0006351) OR regulation of transcription from RNA polymerase II promoter (GO:0006357) OR general RNA polymerase II transcription factor activity (GO:0016251) OR transcriptional activator activity (GO:0016563) OR transcriptional repressor activity (GO:0016564) OR general transcriptional repressor activity (GO:0016565) OR specific transcriptional repressor activity (GO:0016566) OR negative regulator of basal transcription activity (GO:0017163) OR transcription regulator activity (GO:0030528)
  
  See the result of this search (507 not previously identified candidate transcription factors).

Curator's verdict and categorization of transcription factors, and exceptions to it

Curator's verdict and categorization are described on our general information pages.

Novel predictions