Finding the TFs that regulate a set of genes

Question

[kamula]

I've identified a list of co-expressed genes, and I'd like to figure out what is regulating their expression. Currently what I have done is run this group of genes through scope to identify motifs in their promoters. How do I then take those motifs and associate them with a TF? Or is there a better way of solving my problem that you know of?

Answer 1

[TriS]

A good starting point is the ENCODE CHiPSeq significance tools

Starting from a list of genes it looks at published ENCODE data and tells you which TF bind to the region around your gene, you can define the distance you prefer from TSS or gene body

Otherwise, to be a lil more fancy, you can use Homer.

In this case you provide the region you want to analyze (i.e. 2kb up/downstream from your gene) and it will give you a list of TF that can bind the motifs in the regions you queried. it will do it for known and de-novo motifs.

Answer 2

[cpad0112]

Approach 1

• Collect immediate early promoters (1000 bp) --db like promoser
• Run the sequences through the TF databases
• Identify the over represented TFs

Approach 2

• Identify the TFs that are regulated (up or down) in your expression data set
• Correlate the expression of TFs with their target genes (IPA might be helpful in this)

Approach 3

• Collect immediate early promoter elements (1000 bp) --db like promoser
• Submit the sequences to MEME
• See if you could over represented motifs that match with TF motifs (cumbersome)

Answer 3

[Zhilong Jia]

Another tool: Enrichr can make TF enrichment analysis using Transcription Factor PPIs.

Answer 4

[jin]

You can retrieve the regulation among these genes at PlantRegMap for 132 plant species, which also provides a Tool to find enriched TFs in the gene set.