2010 GO camp downstream effect: Difference between revisions

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*Ranjana: Also, like Tanya pointed out, we too annotate to the paper, if you want to say we have annotated every paper that talks about a gene, then you record everything.  Sometimes its hard to tell whether something is a downstream effect.We have no mechanism in place to go back and remove these high-level development terms once the core process/function is known.
*Ranjana: Also, like Tanya pointed out, we too annotate to the paper, if you want to say we have annotated every paper that talks about a gene, then you record everything.  Sometimes its hard to tell whether something is a downstream effect.We have no mechanism in place to go back and remove these high-level development terms once the core process/function is known.
==Annotating to downstream processes==
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! Do you sometimes annotate to downstream processes?*
! *Give an example of when you would AND wouldn't annotate to a DS process
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=3. Proposed annotation policy=
=3. Proposed annotation policy=

Revision as of 08:05, 22 April 2010

1. Background

2. Review of current GO annotation practices

  • Annotating signaling biological processes to transcription factors
  • when not to capture phenotypes : from 22nd Feb Jamboree call [1], Tanya: It's not uncommon for the initial publications to describe a mutant phenotype, with a developmental defect, and then later publications to describe much more explicit functions or processes. You should always annotate based on whatever evidence is available. Once you've done that, the question becomes, "When do we keep or remove the phenotype-based annotations?" At TAIR, their policy is to keep the developmental terms if they think that their users would expect to see them. Some participants suggested that one would expect all orthologs to have the same development-type annotations, across organisms. Others disagreed with this expectation.
  • [From Karen] This is fairly anecdotal. I wasn't able to find papers about this, but it's been known for a long time so that isn't necessarily surprising.

In S. cerevisiae, there are a number of genes which are components of the spliceosome, which when mutated produce strains with defects in protein production/accumulation. Early on, some of these genes were thought to be involved in translation. It was later determined that these genes are components of the spliceosome which are involved in mRNA splicing and not directly in translation at all. The reason why splicing defects produce translation defects is related to the distribution of introns in cerevisiae. Out of about 6000 genes, only about 270 contain introns. Many of the intron containing genes are ribosomal protein genes. Combined with the fact that ribosomal protein genes are highly transcribed, splicing defects have a disproportionate effect on production of ribosomal proteins and thus on translation.

So, while it is true that mutations in many spliceosomal genes produce a phenotype of defects in protein production, it is very clear that this is a downstream effect related to the fact that the majority of mRNAs to be spliced are ribosomal protein genes. Thus, we do not use the mutant phenotype of a defect in protein production to annotate these genes to GO terms related to translation.

  • Ranjana from WormBase: Checking for embryonic lethality or larval stages that do not develop further are very common assays that authors do in the elegans field, such that it may feel like our genes are over-annotated to the terms "embryonic development ending in birth or egg-hatching" and/or "nematode larval development". Sometimes I feel that the body of annotations are getting swamped by these high-level development terms, but I am also uncomfortable ignoring the assay or phenotype, since the authors will devote a good paragraph or table with numbers/percentages to this. Do users come in and search for such terms or ask a question like--give me all the genes that are involved in larval development--we don't know, maybe they do.
  • Ranjana: Also, like Tanya pointed out, we too annotate to the paper, if you want to say we have annotated every paper that talks about a gene, then you record everything. Sometimes its hard to tell whether something is a downstream effect.We have no mechanism in place to go back and remove these high-level development terms once the core process/function is known.

Annotating to downstream processes

3. Proposed annotation policy

4. Examples (papers) and discussion of GO annotation issues

  • Submitted by Pascale: There are several SF items about growth/cell growth/cell proliferation. I know some of the terms were done to accommodate experiments done in Dicty - often people look at the rate of cell proliferation as a general phenotype, and we have been capturing this. It's very high level and usually IMP, but in the absence of other information it seems relevant (otherwise people would not bother testing it).

What do people think about this? To me it's similar to the issue of annotating from IEP or to high level developmental terms by IMP. The question is, what data are too general to be useful to capture?


  • Organismal behaviors are always quite controversial. For example, lonp gene of rat is annotated to aging.

5. Suggestions for Quality Control procedures


Back to 2010_GO_camp_Meeting_Agenda

Name Group Do you always annotate to downstream processes? Do you never annotate to downstream processes? Do you sometimes annotate to downstream processes?* *Give an example of when you would AND wouldn't annotate to a DS process