I have a list of expressed genes. I want to know which gene encodes transcription factor. I cannot search one by one, because there are too many genes. Any suggestions to find genes encoding transcription factors? Any updated database?
I have already checked TFcheckpoint, but its not updated.
2 answers
So you have a list of differentially expressed genes from some experiment? And, you want to know if any of these are transcription factors right? You can retrieve the ontology of all from BIOMART from Ensembl tools and that will give the required results as to which are transcription factors, or translational factors and so on. Also you can use DAVID functional annotation tool to find out if your list has transcription factors or not. https://david.ncifcrf.gov/summary.jsp http://www.ensembl.org/biomart/martview/a48c5d9c7a9a9730c058f330fcba5837
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@c.chakraborty can you kindly explain which attributes are you pointing to in biomart to know about the transcription factors. GO term accession GO term name GO term definition GO term evidence code GO domain If you are talking about these, i still dont see how can i know about the TF?
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ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized. This comment belongs under @c.chakraborty's answer.Find the highest GO term associated with transcription factors and use that as filter in BioMart, along with your gene list.
Hey I am really sorry for the late reply. I will try to help with Biomart- 1. You should have a list of ENSEMBL genes with accession numbers-eg., ENSMUSG00000034384- if you don't, do not worry, take your genes in Entrez from or gene names and use db2db to extract their ensemble ids. 2. Then go to Biomart-http://www.ensembl.org/biomart/martview/7928549e91662fa30732e728fc57cdb6 3. Choose database, mouse strains, ensembl genes 4. Choose dataset-so choose the dataset from your species 5. Then select filters, and paste your ENSEMBL ids at- Input external references ID list 6. Then at attributes select- External- then GO- here you can select GO term accession, name so on 7. Then click reults, which is on the right top. I hope this helps With DAVID. Its fairly easy- 1. Click on functional annotation on right top. 2.Enter your gene in gene list and select the list type you entered in select identifier, like ENSEMBL gene Ids or Entrez Ids etc 3. Select gene list and submit. 4. Click on Functional annotation table and you will know which genes belong to what functional category One thing that I want to remind you is that this process just gives you the GO terms and describes the function of the gene. It has no statistical feature.