Provide support for regulatory sites such as transcription binding sites, promoters

[nathandunn]

This will be done similar to #524 (and is dependent on it) . . . at least initially. We need visualizations for it later that imply a different relationship, as well as new data-types and SO terms.

[cmdcolin]

This might not be super relevant to this issue, but I made a little demo for visualizing some ENCODE data

This is from the chromHMM data from https://sites.google.com/site/anshulkundaje/projects/epigenomeroadmap

Here's what i loaded in JBrowse/WebApollo

Note that this is just using the default CanvasFeatures with some configuration for the colors

This doesn't necessarily help WebApollo add new annotations for these features because it uses CanvasFeatures, but it is a nice visualization. We could possibly convert it to HTMLFeatures though if interested.

This was also inspired by biodalliance.org who also have this visualization

[nathandunn]

@cmdcolin That is pretty sweet. Maybe create a new issue for it WRT to visualizing this type of data and put it in there (is this JBrowse or Apollo?). WRT to this, though, we should explore some of the visualization stuff (heatmaps, variation, etc.).

[selewis]

This needs further discussion. It's not enough to just draw these, we need to consider the relationship they have to genes and each other and the behaviors we'd like to support. Like to hear what Thomas has done for this.

On Mon, Dec 1, 2014 at 10:27 AM, Nathan Dunn [email protected] wrote:

@cmdcolin https://github.com/cmdcolin That is pretty sweet. Maybe create a new issue for it WRT to visualizing this type of data and put it in there (is this JBrowse or Apollo?). WRT to this, though, we should explore some of the visualization stuff (heatmaps, variation, etc.).

— Reply to this email directly or view it on GitHub https://github.com/GMOD/Apollo/issues/32#issuecomment-65110752.

[nathandunn]

Maybe related to #1955

[nathandunn]

I think for this we have to:

• [ ] annotate with / without evidence?
• [ ] relate directly to an isoform
• [ ] provide metadata info similar to other regions

[jrr-cpt]

Would addition of support for promoter features require a relationship to a gene or transcript? We are unlikely to have that data in many cases. However, for some well-studied phages, the promoter boundaries and transcripts are known.

[nathandunn]

@jrr-cpt that is good to know. I'm sure we could have them in isolation. We haven't really thought through the relationship types, so if you have any you explicitly wanted support for that would be helpful.

[jrr-cpt]

The SO term for promoter would be the level we need. Some phage genes use a host prokaryotic promoter, and others a phage RNA pol promoter. These can occur in the same genome, and there is not always a dedicated phage RNA pol.

I'm not sure how the relationships are designated in Apollo. All the SO is_a relationships apply? I can also see including member_of a gene.

[nathandunn]

I think that everything is "is_a" or "part_of" if I recall, but it really depends on how you are exporting it. For a typical GFF3, I'm not sure if it will matter, but potentially that is information we could add to the column 9 metadata.

[jrr-cpt]

IF we were to want to annotate transcipts as feature types, likely we would use transcript and some of its children, like polycistronic transcript

[nathandunn]

Yeah, if you have a list of the transcript types from the SO you want, that would be useful. Attaching promoters to transcripts would have to come in a major new version of Apollo. Adding types and non-coding promoters with no associations would be something we could backport.