extrinsic genotype [GENO_0000524]
A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state. An extrinsic genotype describes variation in the ’expression level’ of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment. The ’extrinsic genotype’ concept is contrasted with the more familiar notion of an ‘intrinsic genotype’, describing variation in the inherent genomic sequence (i.e. ‘allelic state’). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model ’extrinsic’ alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations.
Note
This page displays the raw VFB json record for this term. Please use the link below to open the term inside the Virtual Fly Brain viewerOpen extrinsic genotype in VFB
VFB Term Json
{
"term": {
"core": {
"iri": "http://purl.obolibrary.org/obo/GENO_0000524",
"symbol": "",
"types": [
"Entity",
"Class"
],
"short_form": "GENO_0000524",
"label": "extrinsic genotype"
},
"description": [
"A specification of the known state of gene expression across a genome, and how it varies from some baseline/reference state."
],
"comment": [
"An extrinsic genotype describes variation in the 'expression level' of genes in a cell or organism, as mediated by transient, gene-specific experimental interventions such as RNAi, morpholinos, TALENS CRISPR, or construct overexpression. This concept is relevant primarily for model organisms and systems that are subjected to such interventions to determine how altered expression of specific genes may impact organismal or cellular phenotypes in the context of a particular experiment.\n\nThe 'extrinsic genotype' concept is contrasted with the more familiar notion of an 'intrinsic genotype', describing variation in the inherent genomic sequence (i.e. 'allelic state'). In G2P research, interventions affecting both genomic sequence and gene expression are commonly applied in order to assess the impact specific genomic features can have on phenotype and disease. It is in this context that we chose to model 'extrinsic' alterations in expression as genotypes - to support parallel conceptualization and representation of these different types of genetic variation that inform the discovery of G2P associations."
]
},
"query": "Get JSON for Class",
"version": "44725ae",
"parents": [
{
"symbol": "",
"iri": "http://purl.obolibrary.org/obo/GENO_0000536",
"types": [
"Entity",
"Class"
],
"short_form": "GENO_0000536",
"label": "genotype"
}
],
"relationships": [],
"xrefs": [],
"anatomy_channel_image": [],
"pub_syn": [],
"def_pubs": [
{
"core": {
"symbol": "",
"iri": "http://flybase.org/reports/Unattributed",
"types": [
"Entity",
"Individual",
"pub"
],
"short_form": "Unattributed",
"label": ""
},
"FlyBase": "",
"PubMed": "",
"DOI": ""
}
]
}
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.