TFClass

Lena, Tauras, and Miles

Unless otherwise noted, the information came from the main page of the TFClass website: TFClass

1. Database: TFClass
2. Purpose: To provide a list and classification of human transcription factors based on DNA-binding domains.
3. Biological Information: This database contains a taxonomic key for transcription factors that includes links to other databases (see 11), consensus sequences, and descriptions of what characterizes each motif.
4. Species: At this time, only human transcription factors are included in this database. However, they have considered expanding it to other species, particularly model organisms for insects, plants, and yeast.
5. Biological Questions: This database can be used to determine what human transcription factors bind to particular sites, phylogenetic questions about TF evolution, to inform research on non-coding DNA, and answer a variety of other biological questions. Some specific applications include asking what protein domains cold-shock proteins have in common and determining whether TFs found on the same chromosome are more closely related than those on different chromosomes (found in the Original Paper and through personal creativity).
6. Type of Database: This is a specialty database that focuses in transcription factors. It consists of manually curated meta-data that was obtained from UniProtMaterials and Methods section.
7. TFClass is maintained by Uniprot/SIB (Swiss institute for bioinformatics).
8. This database is funded through FP7 and the federal Ministry of Education and research (BMBF) which are parts of the German government (found in the Original Paper).
9. This Database is an open source database. This means that it can be used by anyone as long as it is properly cited.
10. This database appears to be updated at irregular intervals with the last update being in July 2012. Update periods range from two months to up to a year. This irregularity is likely a result of TFClass's status as a new creation.
11. Once you search for a specific transcription factor or level of the taxonomy, the database will give you links to ProteinAtlas, BIO GPS, Transfac, and/or UniProt (whichever are available).
12. As far as I can tell, the information is available online only and cannot be downloaded. The exception to this is the full taxonomy which can be downloaded as an html document (available here) or Obo Format (available here).
13. The website is not super user-friendly, but it also isn't complex. The website is essentially comprised of one page with a brief explanation of TFClass, a search bar, and a collapsable/expandable tree of transcription factors. There is no help section or tutorial, but there are two questions marks that, when you hover over them with your mouse, will tell you what you can search, and what the "collapse all" and "expand all" buttons do. Searches can only be done by label, ID, or external references, meaning that you cannot type in a sequence of nucleotide bases and see what it is. If you know the ID of the transcription factor you are looking for, it will give you links to outside databases. You can also find links for other levels of the taxonomy and TFs as you expand the tree.