Question: Identify Transcription factor from a list of genes
2
gravatar for Natasha
3.3 years ago by
Natasha40
Natasha40 wrote:

Hello Everyone,

I wish to identify the transcription factors from a list of genes using functional enrichment analysis in DAVID. From which database can I download the set of genes for humans? Is there a database from which I can directly obtain the list of Transcription factors?

Apart from the functional enrichment analysis in DAVID,is there an alternative way of identifying the transcription factors from a set of genes?

genome gene • 2.4k views
ADD COMMENTlink modified 3.3 years ago by Puli Chandramouli Reddy190 • written 3.3 years ago by Natasha40

If you want to just find in your gene list of interest any transcriptiontion factor then consult websites like Pazar, Transfac or AnimalTFdb. However if you want to find upstream TF that binds your genes based on consensus binding pecan,HOMER or iRegulon.

ADD REPLYlink written 3.3 years ago by ivivek_ngs5.1k

Thank you so much for the advice.I am looking for information on the TFs which regulate th eexpression of a given gene. Since TRANSFAC is a commercial platform,I couldn't access it.In pazar, the maximum number of TFs listed is 321 in pleiades project and it's no longer maintained.However,in AnimalTFDB 1544 TFs are listed. I tried accessing the link, given in the paper, of AnimalTFdb. I couldn't access AnimalTFdb (the webpage displays"coming soon")

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Natasha40

I just noticed there is a more recent version of AnimalTFDB(2.0).I am able to access the site.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Natasha40

There you go. You can use that to see if your gene list has any TF but however I would still encourage to find if any TF binds to your list of genes or not. Then that's gives the regulatory consensus.

ADD REPLYlink written 3.3 years ago by ivivek_ngs5.1k

If I understand correctly,the TFs reported in AnimalTFDB are by prediction.I am look for TFs determined solely from experimental observations . Additionally,I am also looking for time course data on how the gene expression varies as a function of TF levels. I would be happy to receive suggestions.

ADD REPLYlink written 3.3 years ago by Natasha40
0
gravatar for Bioaln
3.3 years ago by
Bioaln340
France
Bioaln340 wrote:

https://www.ncbi.nlm.nih.gov/pubmed/20211142, here

ADD COMMENTlink written 3.3 years ago by Bioaln340

Thanks a lot for providing me the link to this article

ADD REPLYlink written 3.3 years ago by Natasha40
0
gravatar for Puli Chandramouli Reddy
3.3 years ago by
Pune, India
Puli Chandramouli Reddy190 wrote:

Hi,

you can upload the list of the geneIDs in uniprot "retrieve/IDmapping" section and then you can browse by "gene ontology " under "View by" heading. Then you can go to "molecular_function" and "sequence-specific DNA binding" (transcription factor" and from here you can get list of transcription factors (transcription factor activity).

ADD COMMENTlink written 3.3 years ago by Puli Chandramouli Reddy190

Thank you so much for your suggestion.I followed the steps mentioned by you after adding the list of genes in retrieve/IDmapping section. These are my list of genes(Entrez gene ID) 25 142 165 166 190 196 257 274 322 323

In the results,it shows 10 out of 10 Entrez Gene (GeneID) identifiers were successfully mapped to 35 UniProtKB IDs in the table below When I click on the "sequence-specific DNA binding", it takes me to this page

Could you please tell me how to find the TFs from the above link?

ADD REPLYlink written 3.3 years ago by Natasha40

Click on the number next to the GO term.

ADD REPLYlink written 3.3 years ago by Puli Chandramouli Reddy190
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