Inferred from High Throughput Genetic Interaction (HGI): Difference between revisions

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== Evidence and Conclusion Ontology ==
== Evidence and Conclusion Ontology ==


[http://www.evidenceontology.org/browse/#ECO_0007003 ECO:0007003 high throughput direct assay evidence used in manual assertion]
[http://www.evidenceontology.org/browse/#ECO_0007003 ECO:0007003 High throughput genetic interaction evidence used in manual assertion]





Revision as of 05:42, 26 February 2018

HTP: Inferred from High Throughput Genetic Interaction

Overview

  • The HGI evidence code is used for annotations based on high throughput experiments reporting the effects of perturbations in the sequence or expression of one or more genes or gene products. HGI is also used for high throughput 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 HGI include high throughput experiments in which the expression of one gene affects the phenotypic outcome of a mutation in another gene.
  • The HGI evidence code is equivalent to the IGI code and he guidelines for annotating using a IGI code should be adhered to.
  • The HGI 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.

Usage

Examples of high throughput assay that should be annotated using this code:

  • Genetic interactions involving two or more mutations that result in suppression or enhancement of a given phenotype, also synergistic (synthetic) interactions
  • Co-transfection experiments in which two or more genes are expressed in a heterologous system to assess functional interaction
  • Expression of one gene alters the phenotypic outcome of a mutation in another gene; the two genes may or may not be from the same species. In the literature, these types of experiments are variably referred to as: functional complementation, rescue experiments, or suppression


More detailed examples on the use of genetic intereaction evidence codes can be found on the IGI page

Evidence and Conclusion Ontology

ECO:0007003 High throughput genetic interaction evidence used in manual assertion


Back to: Guide to GO Evidence Codes