Annotation Conf. Call, March 11, 2014

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Agenda

Present:
SGD:
MGI:
Dicty:
WB:
Pombase:
UCL:
EBI:
Berkeley:
Reactome:
TAIR:
RGD:
Zfin:


Differential Expression Experiments and IEP Evidence Code (Kimberly VA)

  • Background: We recently had a WB user request that we annotate some genes based on the results of differential expression experiments, specifically microarrays and qRT-PCR.
  • In the past, we've been very conservative about annotating to Biological Process terms from differential expression experiments, but this request has raised the issue again and we are re-visiting our annotation practices.
  • In this particular case, these are experiments testing the transcriptional response to infection with pathogenic bacteria although we have a number of similar papers and experiments that examine the transcriptional response to various other stressors, such as oxidative stress, thermal stress, etc.
  • The authors have asked that we annotate the statistically significantly expressed genes to 'defense response' and 'innate immune response'. Note that we had already annotated genes from this paper for which the authors performed follow-up RNAi experiments to try to assess functional significance.
  • Many of these genes do not have other GO annotations and the gene products do not have domains that yield annotations based on sequence aimilarity.
  • Using Textpresso to search the literature, we find that a number of these genes are considered biomarkers for infection response, even in the absence of functional data.
  • We are considering annotating to a high-level response term, e.g. 'response to bacterium', but not to the more descriptive, and functionally suggestive, terms of 'defense response to bacterium' and 'innate immune response'.
  • The issue of annotating based on differential expression experiments has come up before in GO. What are groups currently doing and why, and what, if any, feedback have groups gotten from users wrt these types of annotations? Does GO need to provide more annotation guidelines to curators for this area of annotation?