A DbTF by definition binds to specific DNA sequences in the promoter or enhancer region of a gene and regulates the transcription of the associated gene. Therefore, in our DbTF annotation procedure we considered the following two functional properties as the minimum criteria to qualify a protein as DbTF:
i) there is evidence that the protein binds to specific DNA sequences and
ii) the protein has been demonstrated to be involved in RNAPII dependent regulation of transcription.
Next, we compiled a list of experimental assays for protein-DNA interaction and transcription regulation in order to identify the above evidence types for TFs in scientific publications.
Then we looked for specific scientific publications that would contain evidence to qualify TFs according to our DbTF annotation criteria. We started checking the already existing TF annotations by inspecting the literature that their annotations referred to. The majority of these existing annotations came from GOC, JASPAR and TFCat. Next, we searched the literature for experimental evidence supporting the remaining TF candidates, by performing searches for gene names in the following resources: UniProt, NCBI’s Entrez Gene, iHOP, Gene Cards and NCBI’s PubMed .