finding transcription factors for a list of genes

Question

[avitalwasser]

Hi !

I have a list of genes (Homo sapiens) and I want to find the motifs of the transcription factors that regulate them. For this purpose I need to find the genes' transcription factors first, does anybody know where can I find this data?

thanks, Avital

[pltbiotech_tkarthi]

Try these tools: http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/promoinit.cgi?dirDB=TF_8.3 http://jaspar.genereg.net/search?q=&collection=CORE&tax_group=plants

[ATpoint]

Note that we moved several of your answers back to comments because, as in the past, they mostly consisted of links that can be found by googling the keywords of the toplevel question but no further elaboration or guidance based on hands-on experience.

Answer 1

[ATpoint]

The first step for me would be to identify the region upstream of the transcription start site that is most likely to contain the transcription factor binding sites (= core promoter region). For this, I would get some open-chromatin data (e.g. ATAC-seq from ENCODE or scan GEO/NCBI for datasets) from a closely related cell type and then determine the peak summits for the signal right upstream of the TSS. This should give you a proxy of the region to scan. Once you have the target regions, I would probably use FIMO from the meme suite against the JASPAR2018 core vertebrate collection of transcription factor motifs to identify significant transcription factor motifs. This would be an approach driven by motif occurrence.

Alternatively, you can intersect your promoter regions with the ReMap database, a collection of ChIP-seq derived transcription factor binding sites in human. This would probably be more biologically-correct as motif occurrence alone does not necessarily imply TF binding and some factors may have degenerated or non-canonical motifs that are difficult to detect. You can also try a combination of both approaches of course.

Also make sure to use google and the search function to scan previous threads for ideas:

Determine Transcription Factors For Genes

find transcription factors in a list of genes

Finding transcription factors binding to promoter of a gene or operon in bacteria

Identify Transcription factor from a list of genes

Answer 2

[Nibua]

If you want to begin with motifs, you can have a look at JASPAR website. For all the motifs that are known, you can access to the positions in the human genome. And then cross these locations with your genes.