abnormal transcription elongation phenotype PMID:19328067

[fypoadmin]

NTR abnormal transcription is a NTR abnormal transcription elongation output_of decreased RNA polymerase occupancy at polII gene coding region

A phenotype where the presence of RNA polymerase II is reduced in the coding region (SO:CDS?) vicinity ? Is that too vague?

annotating mcs6 & cdk9 asseyed_using eng1

Original comment by: ValWood

[fypoadmin]

Actually I don't know how to do this......

I have a reduced polII occupance (and I was going to say assayed using eng1, which is the specific gene which was assayed (not all genes are affected).

However, you known't know the context of the "assayed_using" referred to.

I realised theis when, further in in the paper, they measure Cdk9/Pcm1 occupancy along the entire eng1+ gene. So now I'm stuck because we don't want gene specific terms for these.

I could do reduced protein localization to polII gene coding region specific chromatin (or similar) but then how to capture (and distinguish) i) the proteins which were localized to chromatin (here cdk9 & pcm1), and ii) the specific gene region (eng2 CDS).

More specific relations? assayed_using(cdk9),coincident_with_CDS(eng2)

Original comment by: ValWood

[fypoadmin]

For ones that can be pre-composed with SO terms, I use occurs_at for the location. We could add occurs_at to the list of allowed extension relations for FYPO (they're just in a config file that Kim uses with the chado loads).

Original comment by: mah11

[fypoadmin]

Oh yeah, I forgot, that's it (can we use occurs_at with FYPO though, I thought we only used assay_using)

Original comment by: ValWood

[fypoadmin]

we can't at the moment, but it would be very easy to change the config so we can (I even know how to do it)

Original comment by: mah11

[fypoadmin]

Since you want to specify two different things, perhaps it is best to represent this with 2 different phenotypes? e.g. "decreased polII binding to gene specific region" assayed_using(engY) "decreased protein localization to polII transcribed (protein coding?) gene" assayed_using(cdkY)

'genes transcribed by polII' is a very broad group though, it doesn't seem like they have tried very hard to narrow it down..

Original comment by: Antonialock

[fypoadmin]

yeah, Val's asking how to capture 2 kinds of extension for the second annotation -- which protein is localized, and to which gene

Original comment by: mah11

[fypoadmin]

Yeah they did a microarrray and identified some differentially expressed genes (which I have ignored). But they then pick one of these which they know is connected to cell separation, and which this pathway regulates, and they assay the localization of the regulators upstream of polII to the chromatin of the specific gene (eng2). So its simultaneous. The info would be lost by making 2 independent phenotype annotations.

If I lose anything I'd go for the gene, so I can either make the decreased protein localization to chromatin extensions with the proteins in assayed_using.

Then we need to decide if we want to be able to specify specific gene locations using occurs_at....I can wait until we discuss ?

Original comment by: ValWood

[fypoadmin]

new terms so far: abnormal transcription FYPO:0004064 abnormal transcription elongation from RNA polymerase II promoter FYPO:0004065 increased protein localization to chromatin at protein-coding genes FYPO:0004066

comments: I think the "RNA polymerase occupancy" result can be represented using a protein localization annotation, basically the same as the Cdk9 and Pcm1 results but with Rpb1 in the assayed_using extension.

I added the new localization term (FYPO:0004066 above), and since they (conveniently) didn't show any snRNA, miRNA, or other functional RNA genes, I've used "protein coding gene" from SO in the xp. If you find you need something broader, I can do "RNA polymerase II-transcribed regions" without an xp.

I have no problem with occurs_at extensions for specific genes or any other features with PomBase IDs.

I won't do abnormal transcription elongation output_of FYPO:0004066 because there have got to be other ways to get abnormal elongation.

Original comment by: mah11

[fypoadmin]

I'm still forgetting the relations and their use So is there no relationship which can be used between

abnormal transcription elongation and decreased RNA polymerase occupancy at polII gene coding region

Do we have a list of the relations we can use with FYPO (and how) anywhere? I need to get these in my heaad.....

Original comment by: ValWood

[fypoadmin]

First, what's the case for a special term for RNA pol II "occupancy" at all? I still think annotating to "decreased protein localization to chromatin at protein-coding genes" (with a few assayed_using extensions, including rbp2) would be fine for the data in this paper.

Second, if a case can be made for an RNA pol II-specific term, decreased pol II certainly still isn't the only way to get a problem with elongation. So "abnormal elongation output_of decreased pol II" is out.

If decreased pol II along a gene always causes a problem with elongation, then "decreased pol II has_output abnormal elongation" would work.

Original comment by: mah11

[fypoadmin]

Do we have a list of the relations we can use with FYPO (and how) anywhere?

Relations used in FYPO are at the bottom of the OBO files. This morning I've added some usage comments (and done a bit of tidying, which is why it ate the whole morning ... but I digress). I don't want to have to try to keep a separate file or page from drifting out of sync, so I updated the FYPO links on the Useful links wiki page to add a hint (linked file will update when I do a release, i.e. later today).

Original comment by: mah11

[fypoadmin]

Re First, what's the case for a special term for RNA pol II "occupancy" at all? I still think annotating to "decreased protein localization to chromatin at protein-coding genes" (with a few assayed_using extensions, including rbp2) would be fine for the data in this paper.

Yes, I agree. See I could do reduced protein localization to polII gene coding region specific chromatin (or similar) ...I dodn't think of this until later

Original comment by: ValWood

[fypoadmin]

• labels: --> new ontology term
• Description has changed:

Diff:

--- old
+++ new
@@ -1,4 +1,3 @@
-

 NTR abnormal transcription 
     is a NTR abnormal transcription elongation

• status: open --> closed-accepted
• assigned_to: Midori Harris

Original comment by: mah11

[fypoadmin]

Sounds like it's sorted, then -- the new terms should have reached Canto by now, and I did add occurs_at to the config so it's allowed for FYPO extensions.

Closing ...

Original comment by: mah11