SGD Help: Physical and Genetic Interactions
Contents
The Physical and Genetic Interactions page presents detailed
information about physical and genetic interactions for a
particular gene product, along with references for each observation. This page
is linked from the Interactions section
of the Locus Summary page for that gene, where the data are presented in summary form. Data are presented in tabular form on the Physical and Genetic Interactions page. The table is sortable and searchable. More information is available on how to use the table.
All the data may be downloaded to your computer, as tab-delimited
text files, through 'Download' links near the top and bottom of the
page. Additional information for the genes listed can be obtained via
the Analyze gene list options at the bottom of
the page.
Physical and genetic interaction data are presented in a table that contains the
following columns:
- Feature lists the feature name of the protein or gene that was identified in the physical or genetic interaction assay. The feature name is hyperlinked to the Locus Summary page.
- Gene lists the gene name, when available, protein or gene that was identified in the physical or genetic interaction assay. The gene name is hyperlinked to that Locus Summary page.
- Description provides the first part of the description that is listed on the Locus Summary page for the interacting protein or gene.
- Experiment Type indicates the type of physical or genetic interaction. Examples include two-hybrid analysis,
affinity precipitation, affinity chromatography, dosage rescue and synthetic interactions.
- Action indicates whether the gene listed in the
table, or its protein product, was used as
the Bait or identified as the Hit when the interaction was detected.
For example, in a co-immunoprecipitation experiment, the Bait would be
the protein with which the antibodies specifically react; the Hit
would be the protein that interacts with the Bait. In genetic
interaction experiments, the Hit would be the gene identified in the
screen (i.e., a suppressor would always be the Hit). A value of Self
indicates that the protein interacts with itself in a physical interaction.
- Source indicates the source of the data. All of
the physical and genetics interactions are currently bulk-loaded from the BioGRID
database hosted by Mike Tyers' group at the University of Toronto.
Sometimes BioGRID will not yet contain a specific physical
interaction; in that case the interaction is also not yet included in SGD. As of
April, 2006, SGD is regularly updating its interaction data from
BioGRID in order to provide a complete set of interactions from the literature.
- Annotation type indicates whether an interaction was
manually curated from the literature or added as part of a high-throughput dataset.
- Notes are details about the experiment or
additional information that may be useful
in interpretation of the interaction.
- Phenotype indicates the phenotype
that results from the genetic interaction: inviability, slow growth,
etc.
- Reference(s) are published citations that describe the
interaction. If references are missing, we would
greatly appreciate email from the yeast community alerting us to the
correct references.
NOTE: Since the publication of Uetz,
et al. (2000), P. Uetz and colleagues have generated new
physical interaction data. These unpublished interactions are available
at SGD and have been made available to the community via the Yeast
Resource Center. However, these interactions are not part of the Uetz,
et al. (2000)
web supplement. Since the same group identified these
interactions, SGD is citing Uetz, et al. (2000) paper is used as the source of this data.
At the bottom of the page, the 'Analyze gene list' section
provides options for analyzing the genes identified in the genetic and
physical interactions using several different SGD tools. Only genes that are visible
in the table will be included in the list. Remove all filters in
order to include all genes in the analysis.
- The physical interaction and genetic interaction data displayed in
the table can be downloaded as a tab-delimited file via the Data
Download link.
- GO
Term Finder takes a list of genes and finds Gene Ontology (GO) terms that the genes have in common, revealing shared biological
processes, functions, or subcellular locations of the gene products. A
detailed description of the GO Term Finder tool is available on its help
page.
- GO Slim
Mapper maps specific GO terms to broader parent terms (GO Slim
terms), giving an overview of the processes, functions, or cellular
components to which genes in a list are annotated. More information
about the GO Slim Mapper tool is available on its help page.
- Clicking the View GO Annotation Summary link generates a list of all
GO terms to which genes in the interactions table are
annotated. The list is divided into three tables, each containing
terms from one
aspect of GO (biological process, molecular function, cellular
component) and showing how many of the genes in the list are annotated to
each term.
- Expression
Connection searches multiple microarray datasets for gene
expression data for interacting genes. See the
Expression Connection help page
for more information.
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