Frequently Asked Questions
What are transcription factors ?
A TF is a protein that binds the DNA around or overlapping the promoter, affecting gene expression positively and/or negatively depending on operator context and ligand-binding status.
What does the experimental evidence's abbreviations mean?
In the general table we provide a detailed description of each abbreviation.
What is the domain organization of TFs?
In general, TFs are two-domain proteins, however, there are some cases where TFs are composed of a mono-domain or proteins with a large number of domains.
What is the experimental evidence considered in this work?
We have considered the following experimental evidence described in 2787 references.
How can I get the complete dataset of proteins?
All information is available to the community. Sequences can be obtained in FASTA format and information in text format. If you want the complete database in .csv format, please contact us at ernesto.perez@iimas.unam.mx
I have a protein that is a TF. How can I add it to the Entraf database?
Please contact us at ernesto.perez@iimas.unam.mx if you have another protein to suggest for inclusion in the Entraf database.
I would like to use the Entraf database in a project to analyze the amino acid sequences or structures using bioinformatics.
Please contact us at ernesto.perez@iimas.unam.mx if you are interested in using the ENTRAF database.
About EnTRaF
The DNA-binding transcription factors (TFs) have a fundamental role to contend with environmental changes in all the organisms. These proteins affect gene expression positively and/or negatively depending on operator context and ligand-binding status. Prediction and characterization of novel TFs generally involve finding a function for a protein considering a reference dataset (golden standard), which include the information of well-annotated proteins with experimental evidence.
ENTRAF provides a centralized, web-based location to organize information about 1784 TFs with experimental evidence, from bacteria and archaea organisms, collected from Swissprot, PDB, RegulonDB, RegulomeDB, CollecTF, and DBTBS.
ENTRAF version 2.0 contains 2787 references associated with 1784 Transcription factors (TFs). From these, 1712 TFs have been characterized in 29 bacterial orders, such as Gammaproteobacteria, Bacilli, and Actinomycetota; and 72 TFs in ten archaeal orders, as Thermoprotei and Thermococci.