Add new TF binding motif to website list

[ValWood]

new TF binding motif to add

5ʹ-CGNMGATCNTY-3

Loz1

https://www.ncbi.nlm.nih.gov/pubmed/31515876

[ValWood]

actually it's a promoter element with consensus CGNNGATCNTT and GNNGATC

[Antonialock]

is that for tyhe TF binding site page or for the promoter track that we generate? Whats the difference between the short and long motif?

[ValWood]

TF binding site page first.

Good point. I forgot about the tracks.

This is a prequisite to create a track (this list is used).

I guess every time there are a few new motifs the track should be regenerated. I forgot how this happens (@kimrutherford have you ever run this or has it not been regenerated since Ensembl?)

[Antonialock]

I think Kim regenerated it once not that long ago.

Maria had a student look at all pombe TF binding sites. I must remember to look at this to see if we need to update our consensus motifs (or review them - sometimes you see variations in the literature, so we should make sure to pick the 'best' version)

On Wed, Oct 9, 2019 at 5:19 PM Val Wood notifications@github.com<mailto:notifications@github.com> wrote:

TF binding site page first.

Good point. I forgot about the tracks.

This is a prequisite to create a track (this list is used).

I guess every time there are a few new motifs the track should be regenerated. I forgot how this happens (@kimrutherfordhttps://github.com/kimrutherford have you ever run this or has it not been regenerated since Ensembl?)

[ValWood]

Yes, I suggest this is a multi step.

• Update the motifs page
• Extend page using Maria's
• Ask pombelist if they know of any additional (and find a more prominent place to host the list)
• Open a ticket for @kimrutherford to regenerate tracks (once the other steps are completed)

[Antonialock]

good plan! will make tickets!

[Antonialock]

Could you comment: Whats the difference between the short and long motif?

[ValWood]

Could you comment: Whats the difference between the short and long motif?

O right. I had assumed it was 2 motifs, but one is a short version.

I would just use the long version.

[ValWood]

SO term now exists for Loz1

[Antonialock]

added SO:0002225

[Antonialock]

ps it overlaps with zinc repressed element|GNMGATC

[ValWood]

Oh, is it even any different. Same authors, same TF????

[ValWood]

I'm checking the difference with Amanda.