Finding target genes of a TF

Question

[hodatn]

How Can I Find Target Genes Of A Transcription Factor in plants? I mean I need databases that do this job for plants TFs. (I have RNA-seq Data)

[Satyajeet Khare]

1. Look for public ChIP-Seq datasets of the TF of your interest (preferably, in the tissue of your interest)
2. Look for RNA-Seq datasets of TF-KO.

Combined analysis should provide lots of clues. If the above datasets are not available, get the TF motif and check if your target genes have it in their regulatory regions.

[hodatn]

Thank you. But what do you mean by " TF-KO"? Would you please explain more, or put the links of the databases that are able to find Target genes of a TF?

[Satyajeet Khare]

KO: Knockout. You can also use KD (knockdown) datasets.

[Michael]

You have provided insufficient context to resolve your question:

• which plant(s): species, genomes, etc.
• which TF (a specific one?)
• what kind of RNA-seq data

Why didn't you describe your problem in detail in the first place?

Answer 1

[Alex Reynolds]

Given sequence data, you can discover binding sites with, say, FIMO and a database of (plant) TFs (such as JASPAR CORE Plantae).

Once you have binding site locations, you can map them with BEDOPS, using bedops to generate the space of gene promoters (say 500-1000 bases upstream of the gene TSS) and using bedmap to map the transcription factor binding sites to the gene promoter regions.

[hodatn]

Thank you so much.Well,actually I have some TFs, I need to find: 1) in what networks they exist? 2) Find their modules, 3)find their target genes, 4) and find all their binding sites, The JASKAR CORE Plantae that you introduced is helpful, But I don't know how should I work with BEDOPS!!!