#29 question re ECO:0000296 and 297

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nobody
None
5
2012-04-20
2012-04-20
No

Hi Marcus,

I'm looking for terms to describe experiments that look at reporter gene product activity or abundance (lacZ or GFP) as a measure of transcriptional activation. The closest terms I can find in ECO are these:

ECO:0000296
green fluorescent protein transcript localization evidence
A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene.

ECO:0000297
LacZ transcript localization evidence
A transcriptional activation assay that uses a LacZ reporter gene.

and the definitions are accurate but not the term names, since the localization of the transcripts was not looked at. Are there more appropriate terms that I'm missing? Or do we need new terms?

Thanks!
Maria

Discussion

  • Marcus

    Marcus - 2012-04-20

    Hello Maria,

    I see what you are saying. I think that the appropriate course of action here would be to narrow the definition of the existing terms to specifically refer to localization and then to create two new terms corresponding to each GFP and LacZ term that addresses the quantification you mention. For example, ECO:0000296 should be "Evidence from a transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene to detect localization of a protein" (or some similar phrase that refers to the localization. ECO:0000XXX GFP would be something like "Transcriptional activation assay evidence where green fluorescent protein (GFP) abundance or activity are quantified as a measure of transcriptional activation."

    ECO:0000296 should probably be moved at that time, because it would not be a "transcriptional activation assay".

    Alternatively, we could redefine the LacZ/GFP terms to specifically refer to transcriptional activation; then they wouldn't need to be moved. We could create two new terms corresponding to localization.

    Which of these ideas do you think would be best? Just curious--I'll still have to see who else/how these are being used.

    Marcus

     
  • Antonia Lock

    Antonia Lock - 2012-04-23

    Marcus,
    since you're interested in what others are using.

    I've used;
    id: ECO:0000049
    name: reporter gene assay evidence
    def: "Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response." [TAIR:TED]
    synonym: "IEP: expression of a reporter gene" RELATED []
    is_a: ECO:0000059 ! experimental phenotypic evidence

    for these types of experiments.

     
  • Maria C. Costanzo

    Hi Marcus,

    I don't have a strong opinion about the way to resolve this; either of the ways you proposed sounds fine to me, and I'd also be ok with using the more general term that Antonia suggested. Whatever works!

    Thanks,
    Maria

     

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