Hi! I'm really sorry for my ignorance, but I'm still a student. Is there any database where I could find a transcription factor whose target genes are still unknown? Thank you so much for your time.
https://sra-explorer.info/ can query NCBI for datasets. If you do not find the TF there plus not via google then chances are good no one has ever ChIPed it. At what kind of level are you? PhD Student? ChIP-seq can be tricky, laborious and expensive especially with non-standard TF targets for which no validated antibodies exist and you would need to try different non-ChIP-grade ABs. Is this really what your assignment is?
Also, for human there is ReMap, a database that collects most of published human ChIP-seq datasets and then provides peak lists etc. This (from what I know) also covers most of ENCODE datasets which Alex Reynolds suggested above. If you do not find datasets for a specific TF in there plus not via sra-explorer I would be reasonably sure that TF has not been extensively studies in a genome-wide fashion.
Hi! I'm really sorry for my ignorance, but I'm still a student.
No, I am sorry that you feel that you had to introduce your question in this way.
In addition to my colleague's suggestion(s), please explore TRANSFAC.
Also, be sure to search previous Biostars questions. For example:
Kevin
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Maybe it is easier to help if you say what the project is. This question is very broad. Target genes can be defined by performing ChIP-seq analysis followed by intersection of TF bindingsites with promoters or nearby distal regulatory elements. Still, this is highly cell-type and context dependent.
I have to choose a transcription factor in order to discover its target genes, and develop a RNA-seq coupled with ChIP-seq experiment. And I need to be sure that there haven't been made any previous ChIP-seq experiments.
The ENCODE project offers ChIP-seq experiment results for various published TFs (example). Perhaps this tool might be generally useful in narrowing down TFs that meet your criteria.