Difference between revisions of "TFClass"
From LMU BioDB 2013
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# Database: [http://tfclass.bioinf.med.uni-goettingen.de/tfclass TFClass] | # Database: [http://tfclass.bioinf.med.uni-goettingen.de/tfclass TFClass] | ||
# Purpose: To provide a list and classification of human transcription factors based on DNA-binding domains [http://tfclass.bioinf.med.uni-goettingen.de/tfclass *]. | # Purpose: To provide a list and classification of human transcription factors based on DNA-binding domains [http://tfclass.bioinf.med.uni-goettingen.de/tfclass *]. | ||
| − | # | + | # 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. |
| + | # 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. | ||
| + | # Biological Questions: This database can be used to determine what human transcription factors bind to particular sites and as a portal to find transcription factors in. It is also a method to track homology in transcription factors and find which may act upon a specific gene sequence. (needs work--will talk to Dr. Dahlquist tomorrow) | ||
| + | # Type of Database: This is a specialty database that focuses in transcription factors. It consists of manually curated meta-data that was obtained from UniProt[http://nar.oxfordjournals.org/content/41/D1/D165.full.pdf+html Materials and Methods section]. | ||
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:11.) Once you search for a specific transcription factor, the database will give you links to that sequence on ProteinAtlas, BIO GPS, Transfac, and Uniprot. | :11.) Once you search for a specific transcription factor, the database will give you links to that sequence on ProteinAtlas, BIO GPS, Transfac, and Uniprot. | ||
:12.) As far as I can tell, the information is available online only and cannot be downloaded. | :12.) As far as I can tell, the information is available online only and cannot be downloaded. | ||
Revision as of 06:11, 26 September 2013
- Database: TFClass
- Purpose: To provide a list and classification of human transcription factors based on DNA-binding domains *.
- 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.
- 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.
- Biological Questions: This database can be used to determine what human transcription factors bind to particular sites and as a portal to find transcription factors in. It is also a method to track homology in transcription factors and find which may act upon a specific gene sequence. (needs work--will talk to Dr. Dahlquist tomorrow)
- 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.
- 11.) Once you search for a specific transcription factor, the database will give you links to that sequence on ProteinAtlas, BIO GPS, Transfac, and Uniprot.
- 12.) As far as I can tell, the information is available online only and cannot be downloaded.
- 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.
Lena (talk) 17:40, 25 September 2013 (PDT)
Tauras: 1-6 Miles: 7-10 Lena: 11-13
First Draft by 11:30 Wednesday, Editing on Thursday
