a more complex motif for your poster?

[paul-shannon]

Hi @mariam16548

Today let's create a full-chromosome or maybe even whole genome study of a transcription factor (TF) with more length (and thus more binding complexity) that GATA1. We might explore some of the TFs which play a role in Alzheimer's Disease (AD). PKNOX2 is a possibility if there is ChIP-seq in our database. Pictured below. Note the complexity of the motif - that's what we'd like to use.

Then we can work together to

• obtain all its ChIP-seq binding sites
• get FIMO scores on each
• create some good graphics highlighting the variability of FIMO scores
• the graphics will be useful for your poster

[paul-shannon]

@mariam16548 Here is a histogram and a motif logo for your poster. I think they summarize our work nicely - and therefore also provide a good basis for us to discuss as you solidify your grasp of all the concerts involved.

The histogram demonstrates that

• we find only a few high-quality (pval 10e-6 or smaller) matches of our motif in the ChIP-seq regions
• most of the motif matches score between 10e-1 and 10e-2 (0.1 to 0.01) - a low measure of statistical significance.
• 459 ChIP-seq regions have no match at all.

The R script which creates the graph is in this repo

github/chip-seq-motif-study/explore/tead1/tead1.R