Experimental Evidence Codes
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experimental_systems [2018/07/27 16:35] jenn [Genetic Interactions] |
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| ====== Experimental Evidence Codes ====== | ====== Experimental Evidence Codes ====== | ||
| BioGRID interactions are recorded as relationships between two proteins or genes (i.e. they are binary relationships) with an evidence code that supports the interaction and a publication reference. The term “interaction” includes, as well as direct physical binding of two proteins, co-existence in a stable complex and genetic interaction. It should not be assumed that the interaction reported in BioGRID is direct and physical in nature; the experimental system definitions below indicate the nature of the supporting evidence for an interaction between the two biological entities. It should also be noted that some interactions in BioGRID have various levels of evidential support. BioGRID simply curates the result of the experiment from the publication and we do not guarantee that any individual interaction is true, well-established or the current consensus view of the community. Curating all available evidence supporting for an interaction enables orthogonal data from various sources to be collated, allowing users of the database to decide confidence in the existence and/or physiological relevance of that interaction. | BioGRID interactions are recorded as relationships between two proteins or genes (i.e. they are binary relationships) with an evidence code that supports the interaction and a publication reference. The term “interaction” includes, as well as direct physical binding of two proteins, co-existence in a stable complex and genetic interaction. It should not be assumed that the interaction reported in BioGRID is direct and physical in nature; the experimental system definitions below indicate the nature of the supporting evidence for an interaction between the two biological entities. It should also be noted that some interactions in BioGRID have various levels of evidential support. BioGRID simply curates the result of the experiment from the publication and we do not guarantee that any individual interaction is true, well-established or the current consensus view of the community. Curating all available evidence supporting for an interaction enables orthogonal data from various sources to be collated, allowing users of the database to decide confidence in the existence and/or physiological relevance of that interaction. | ||
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| + | For additional details on BioGRID ontologies such as our evidence codes, visit our **[[https://github.com/BioGRID/BioGRID-Ontologies|ontology repository at Github]]**. | ||
| Interactions are recorded under the experimental systems described below: | Interactions are recorded under the experimental systems described below: | ||
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| * **Co-localization** - An interaction is inferred from two proteins that co-localize in the cell by indirect immunofluorescence only when in addition, if one gene is deleted, the other protein becomes mis-localized. This also includes co-dependent association of proteins with promoter DNA in chromatin immunoprecipitation experiments (write "ChIP" in qualification text box), and in situ proximity ligation assays (write "PLA" in qualification text box). | * **Co-localization** - An interaction is inferred from two proteins that co-localize in the cell by indirect immunofluorescence only when in addition, if one gene is deleted, the other protein becomes mis-localized. This also includes co-dependent association of proteins with promoter DNA in chromatin immunoprecipitation experiments (write "ChIP" in qualification text box), and in situ proximity ligation assays (write "PLA" in qualification text box). | ||
| - | * **Co-purification** - An interaction is inferred from the identification of two or more protein subunits in a purified protein complex, as obtained by several classical biochemical fractionation steps, or else by affinity purification and one or more additional fractionation steps. Note that a Western may also be used to identify the subunits, but that this differs from "Affinity Capture-Western" because it involves at least one extra purification step to get rid of contaminants. Typically, TAP-tag experiments are considered to be affinity captures and not co-purification experiments. If there is no obvious bait-hit directionality to the interaction, then the co-purifying proteins should be listed as a complex (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15907469&query_hl=4&itool=pubmed_DocSum|PMID: 15907469]]). If only co-fractionation is demonstrated, i.e. if the interaction is inferred from the presence of two or more protein subunits in a partially purified protein preparation (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11294905&query_hl=4&itool=pubmed_DocSum|PMID: 11294905]], Fig. 9), then use "Co-fractionation" instead. | + | * **Co-purification** - An interaction is inferred from the identification of two or more protein subunits in a purified protein complex, as obtained by several classical biochemical fractionation steps, or else by affinity purification and one or more additional fractionation steps. Note that a Western or mass-spec may also be used to identify the subunits, but that this differs from "Affinity Capture-Western" or "Affinity Capture-Mass Spec" because it involves at least one extra purification step to get rid of contaminants (e.g. [[https://www.ncbi.nlm.nih.gov/pubmed/19343713?dopt=Abstract|PMID: 19343713]]). Typically, TAP-tag experiments are considered to be affinity captures and not co-purification experiments. If there is no obvious bait-hit directionality to the interaction, then the co-purifying proteins should be listed as a complex. If only co-fractionation is demonstrated, i.e. if the interaction is inferred from the presence of two or more protein subunits in a partially purified protein preparation (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11294905&query_hl=4&itool=pubmed_DocSum|PMID: 11294905]], Fig. 9), then use "Co-fractionation" instead. |
| * **Far Western** - An interaction is inferred when a bait protein is immobilized on a membrane and a prey protein that is incubated with the membrane localizes to the same membrane position as the bait protein. The prey protein could be provided as a purified protein probe (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12857883&query_hl=4&itool=pubmed_DocSum|PMID: 12857883]], Fig. 7). | * **Far Western** - An interaction is inferred when a bait protein is immobilized on a membrane and a prey protein that is incubated with the membrane localizes to the same membrane position as the bait protein. The prey protein could be provided as a purified protein probe (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12857883&query_hl=4&itool=pubmed_DocSum|PMID: 12857883]], Fig. 7). | ||