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--- experimental_systems [2018/07/27 16:10]
jenn [Physical Interactions]
+++ experimental_systems [2018/08/06 09:16]
jenn [Physical Interactions]
@@ Line 22: / Line 22: @@
   *  **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).
@@ Line 43: / Line 43: @@
 ===== Genetic Interactions =====
-  *  **Dosage Growth Defect** - A genetic interaction is inferred when over expression or increased dosage of one gene causes a growth defect in a strain that is mutated or deleted for another gene.
+  *  **Dosage Growth Defect** - Overexpression/increased dosage of one gene causes a growth defect in a strain that is mutated/deleted for another gene (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15166139&query_hl=4&itool=pubmed_DocSum|PMID: 15166139]]).
-  *  **Dosage Lethality** - A genetic interaction is inferred when over expression or increased dosage of one gene causes lethality in a strain that is mutated or deleted for another gene.
+  *  **Dosage Lethality** - Overexpression/increased dosage of one gene causes lethality in a strain that is mutated/deleted for another gene (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10805723&query_hl=4&itool=pubmed_DocSum|PMID: 10805723]], Fig. 3).
-  *  **Dosage Rescue** - A genetic interaction is inferred when over expression or increased dosage of one gene rescues the lethality or growth defect of a strain that is mutated or deleted for another gene.
+  *  **Dosage Rescue** - Overexpression/increased dosage of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12207708&query_hl=4&itool=pubmed_DocSum|PMID: 12207708]], Fig. 3).
-  *  **Negative Genetic** - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition. This term is reserved for high or low throughput studies with scores.
+  *  **Negative Genetic** - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20093466&query_hl=4&itool=pubmed_DocSum|PMID: 20093466]]).  This term is reserved for high or low throughput studies with scores.
-  *  **Phenotypic Enhancement** - A genetic interaction is inferred when mutation or overexpression of one gene results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.
+  *  **Phenotypic Enhancement** - Mutation/deletion/overexpression of one genes results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene, for example response to DNA damage or transcriptional output (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11890933&query_hl=4&itool=pubmed_DocSum|PMID: 11890933]], Fig. 2).
-  *  **Phenotypic Suppression** - A genetic interaction is inferred when mutation or over expression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.
+  *  **Phenotypic Suppression** - Mutation/deletion/overexpression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10073572&query_hl=4&itool=pubmed_DocSum|PMID: 10073572]]).
-  *  **Positive Genetic** -  Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a less severe fitness defect than expected under a given condition. This term is reserved for high or low throughput studies with scores.
+  *  **Positive Genetic** -  Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a less severe fitness defect than expected under a given condition.(e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20093466&query_hl=4&itool=pubmed_DocSum|PMID: 20093466]]).  This term is reserved for high or low throughput studies with scores.
-  *  **Synthetic Growth Defect** - A genetic interaction is inferred when mutations in separate genes, each of which alone causes a minimal phenotype, result in a significant growth defect under a given condition when combined in the same cell.
+  *  **Synthetic Growth Defect** - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a significant growth defect under a given condition (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12871902&query_hl=4&itool=pubmed_DocSum|PMID: 12871902]], Fig. 8).
-  *  **Synthetic Haploinsufficiency** - A genetic interaction is inferred when mutations or deletions in separate genes, at least one of which is hemizygous, cause a minimal phenotype alone but result in lethality when combined in the same cell under a given condition.
+  *  **Synthetic Haploinsufficiency** - A genetic interaction is inferred when mutations or deletions in separate genes, at least one of which is hemizygous, cause a minimal phenotype alone but result in lethality when combined in the same cell under a given condition (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=17167106&query_hl=4&itool=pubmed_DocSum|PMID: 17167106]]).
-  *  **Synthetic Lethality** - A genetic interaction is inferred when mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in lethality when combined in the same cell under a given condition.
+  *  **Synthetic Lethality** - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in lethality under a given condition (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14690608&query_hl=4&itool=pubmed_DocSum|PMID: 14690608]]).
-  *  **Synthetic Rescue** - A genetic interaction is inferred when mutations or deletions of one gene rescues the lethality or growth defect of a strain mutated or deleted for another gene.
+  *  **Synthetic Rescue** - Mutation/deletion of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene (e.g. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14734533&query_hl=4&itool=pubmed_DocSum|PMID: 14734533]], Fig. 1).

Experimental Evidence Codes

Differences