Inferred from High Throughput Genetic Interaction (HGI)
HTP: Inferred from High Throughput Genetic Interaction
- 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.
- Notes on what qualifies as high throughout data and general annotation guidance for high throughout experiments can be found on the HTP evidence code page.
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
Note: High numbers of potential annotations should not be used as a absolute indicator of whether an experiment warrants a HGI code. Sometimes large-scale genetic screens are aimed at comprehensively dissecting the process rather than a hypothesis-free probe. A detailed case-by-case review needed by curator to determine the methods and intent of the experiments.
Evidence and Conclusion Ontology
Last reviewed: February 26, 2018