Annotation Conf. Call 2016-02-08

Agenda

Bluejeans Conference Line

• Recurring meeting URL: https://bluejeans.com/993661940

Review New IGI Documentation

• Following on from the 2016-01-12 call where we discussed how to annotate co-transfection experiments, below is a draft of new IGI documentation for curation.
• For this call, I'd like to review the new documentation, and solicit input for examples.
• For reference, here is the link to the existing documentation on the web site: http://geneontology.org/page/igi-inferred-genetic-interaction

    IGI: Inferred from Genetic Interaction

    •	Genetic interactions such as suppression, enhancement, synergistic (synthetic) interaction, etc.
    •	Co-transfection experiments
    •	Functional complementation
    •	Phenotypic rescue??  Formerly ‘Rescue experiments’. Does this refer to multicopy suppressors?
    •	Inference about one gene drawn from the phenotype of a mutation in a different gene??

 The IGI evidence code is used for annotations based on experiments reporting the effects of perturbations in the sequence or         expression of one or more genes or gene products.  IGI is also used for experiments that interrogate functional    interactions between   two or more genes or gene products when co-expressed, for example, in a cell line.  Additional uses of IGI include functional complementation experiments, genetic redundancy, phenotypic rescue, and inferences made about one gene drawn from the phenotype of mutations in a different gene.  

    Key to deciding whether or not to use the IGI or IMP (Inferred from Mutant Phenotype) evidence code is consideration of the point of reference (i.e., what is being compared) to determine a possible interaction.  If experiments interrogate the effects of multiple mutations or differences from the control, then use IGI.  If experiments interrogate the effects of a single mutation or difference from the control, then use IMP.

    The IGI evidence code requires curators enter a stable database identifier for the interacting entity in the With/From field of the Gene Association File (GAF).  Independent interactors may be captured in the With/From field by separating each entry with a pipe.  If the interaction experiment involves multiple perturbations simultaneously, e.g. triply mutant strains, then the respective interactors are separated with a comma.

    Genetic interactions such as suppression, enhancement, synergistic (synthetic) interactions, etc.

    This use of the IGI evidence code refers to the more “traditional” genetic interaction experiments performed in model organisms, such as Saccharomyces cerevisiae, as well as more recent approaches adopted in a number of different systems such as RNA-mediated knockdown or genome editing techniques.  Note that genetic interaction experiments may be performed with both loss- and gain-of-function mutations.  Consequently, curators will need to use their expertise to determine whether interaction phenotypes resulting from gain-of-function mutations are informative about the normal, wild type role of a gene or gene product. 

Example 1: Loss-of-function mutations

       Need example - David H. ?

Example 2: Gain-of-function mutations

Axon regeneration following injury requires the activities of MAP kinase and cAMP signaling pathways that promote, amongst other things, microtubule dynamics and growth cone formation. In C. elegans, the activity of the upstream-most kinase in one of the MAPK signaling pathways, DLK-1, is stimulated by Ca2+ influx mediated by the EGL-19 voltage-gated calcium channel. EGL-19’s regulatory role in the MAPK-mediated axon regeneration pathway was determined, in part, through doubly mutant animals containing an egl-19 gain-of-function mutation and a dlk-1 loss-of-function mutation that showed a reduced axon regenerative response when compared to egl-19(gf) alone. PMID:20203177

EGL-19 positive regulation of MAPK cascade involved in axon regeneration (GO:new) IGI DLK-1

Note that in this example, reciprocal IGI annotations are not made, as the GO term selected for EGL-19 does not make sense for DLK-1.

Example 3: Synergistic (synthetic) interactions

Disruption of the MSB2 gene in S. cerevisiae has no appreciable effects on the cell's ability to activate the High-Osmolarity Glyceral (HOG) pathway upon osmotic stress, or on cellular growth on high-osmolarity media. To identify potential osmosensors in the SHO1 branch of the HOG pathway, the authors screened for a mutant that is osmosensitive only in an msb2Δ background and recovered mutations in the HKR1 gene. Like MSB2, mutations in HRK1 alone confer no osmosensitivity to the cells. PMID:17627274

MSB2 hyperosmotic response (GO:0006972) IGI HKR1

             HKR1  hyperosmotic response (GO:0006972)  IGI  MSB2