Video Tip of the Week: AnimalTFDB for transcription factors

Transcription factor details–and sources of information about them and their binding sites–are definitely among the the most common questions we hear in our workshops. There are ways to look at predictions of binding, and for some species evidence of binding, and there are ways to look for binding motifs. But these resources vary in methods and scope, and it’s not easy to obtain collected information about transcription factors in many species.

One group has tried to change this, at least for animal transcription factors, with the AnimalTFDB. They collected and curated information about more than 70 families of TFs from 50 species, and created an interface where you can explore this collection by family, by species, and more.

This was offered as one of the sources of information from a recent query at BioStar. The poster was looking specifically for non-model organism information, and this database was one of the suggestions. But you can explore that question for other details and suggestions too.

The paper from the AnimalTFDB team provides information on other sources of TF information–including bacteria, plants, and various types of related resources too. So if you are looking for non-animal details there could be some guidance for you in there. Some of these you might see in future tips!

In the AnimalTFDB system itself, you’ll find that you have multiple ways to explore the data. From the landing page you can quickly browse to the collected data by TF family, or move right to the data organized by species instead. But there is also a standard search option with a form-based query. You can refine your search in various ways with that search form.

When you get to a transcription factor (or one of the other types that’s curated, transcription co-factors and chromatin remodeling proteins) there will be links to many types of useful additional details. Transcripts, domains, GO terms, and links to multiple related resources and more.

So if you are interested in transcription factors, co-factors, and chromatin remodeling proteins in animal species, check out AnimalTFDB.

Quick link:

AnimalTFDB: http://www.bioguo.org/AnimalTFDB/

Reference:
Zhang, H.M., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H. & Guo, A.Y. (2011). AnimalTFDB: a comprehensive animal transcription factor database, Nucleic Acids Research, 40 (D1) D149. DOI: 10.1093/nar/gkr965