During my current research, I need to find Transcription Factors of a gene. I have the promoters of it listed but can not find a way to research about what TF bind to that promoter of that gene. How can I do that?
The easiest approach to find transcription factors for any given organism is based on sequence homology with other known transcription factors that bind similar promoters for similar functions. In order for this to work your organism of interest must be sequenced. http://smart.embl-heidelberg.de/
You can also try Yeastract web tool ( http://www.yeastract.com/ ), the "Transcription Factors" function of GeneCodis ( http://genecodis.cnb.csic.es/ ) , or https://www.researchgate.net/deref/https%3A%2F%2Fgeneregulation.org%2Fprotein-dna-binding%2F
Hi Emirhan to add to the comment of Nicolo, there are several ways to try to find with transcription factors (TFs) bind on the promoters regions. If you dont have coding experience I recommend that you check the UCSC browser downloadable track of JASPAR 2022 in your specie of interest. If you have some coding experience, you can prepare a multi fasta file with the promoters of interest and run FIMO (Grant et al., 2011) from the MEME suite and select depending on your organism the defined transcription factor binding sites databases JASPAR CORE 2022,Jolma 2013,Swiss regulon ... there are several. You can chose depending if you want to use a TF database experimentally validated or not and the organism.
Hi Emirhan, I truly recommend the strategy proposed by Mar Muniz Moreno. If you have some coding experience, the biomaRt package in R (https://bioconductor.org/packages/release/bioc/html/biomaRt.html) allows to download the promoter sequences as a FASTA file (exportFASTA: https://rdrr.io/bioc/biomaRt/man/exportFASTA.html) which you can directly input in MEME, either the command line or web based version, as previously suggested. To add to Mar reply, once you have the MEME results, you can check your results and Transcription factors binding sites through Factorbook, a transcription factor (TF)-centric web-based repository of integrative analysis associated with ENCODE ChIP-seq data (https://www.factorbook.org).