Finding differential enrichment of known motif in gene set

Question

[omansn]

Hello everyone,

First, thank you for any help, I am not a bioinformatician so pardon my amateur question.

I read a paper (cited below) that identified a ~28 nt motif that varies (but has a conserved 5-GTGG-3, and adjacent 5-T-A-3 region). This motif is interesting because it forms a stem-loop that causes rapid depurination of the G residue.

I have a set of ~1,100 related genes (file is 1.2mb) and I want to look to see if this motif is enriched in this family of genes compared to the rest of the genome.

So far I've explored a couple options including MEME suite, but my data set is too large. Does anyone have any other ideas? This doesn't seem to be a common analysis.

Amosova, O, Coulter, R, Fresco, J.R. (2006) Self-catalyzed site-specific depurination of guanine residues within gene sequences. PNAS 103:12, 4392-4397

[omansn]

I should add that multiple programs that I have found can do a differential analysis for known motifs (e.g.GO, PANTHER) but I have been unable to find this motif in the classification system of known motifs. Thus, I think I will need to use a .fa, or .txt of the sequence (I think?).

Thanks!

Answer 1

[Zhilong Jia]

I recommend the tool enrichr, and what you need is just the gene SYMBOLs, then choose the trscrption item and then choose the second transfac and jaspar PWM. it's easy.

Answer 2

[TriS]

You can try Homer, it looks for both known and de-novo motifs based on coordinates that you provide.

it's a little tricky to install (and you need either Mac or Linux or Cygwin running on windows), but it's a very useful tool. there is a good step by step guide on how to install it, don't forget to install all the necessary/complementary software that Homer works with, they are all listed on the Homer's page.