SGD Help: Physical and Genetic Interactions
The 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, and also from the Interactions tab at the top of the Locus Summary. Data are presented in multiple ways - a summary graph, tabular table, and a network diagram.
All data may be downloaded as a tab-delimited text file by clicking the 'Download' button near the bottom of the 'Annotations' table. Additional information for the genes listed can be obtained through the 'Analyze' button underneath the table. A file containing interaction data, interaction_data.tab, for all genes is available for download.
- Interaction data
- The Interactions page
- Searching and browsing interaction data
SGD's interaction data encompasses protein-protein and protein-RNA interactions, as recorded by the Biological General Repository for Interaction Database (BioGRID). BioGRID is a repository of interaction data manually curated from scientific literature for Saccharomyces cerevisiae as well as other organisms. BioGRID interactions are binary relationships between two proteins or genes. Interactions include physical and genetic interactions. Physical interactions are defined as the direct physical binding of two proteins, or co-existence in a stable complex, whereas genetic interactions are interactions between two or more mutants. For more details about BioGRID's curation process, see here.
The overlap of physical and genetic interaction annotations are summarized in a Venn diagram. Genes in physical, genetic, overlapping, and both lists can be analyzed by selecting the desired list with the 'Physical', 'Genetic', 'Intersecting', or 'All' button, below the summary diagram. These buttons go to an 'Analyze' page to look at Gene Ontology enrichment, expression, and other data about these genes.
The Annotations table contains the following columns: Interactor, Type, Assay, Annotation, Action, Modification, Phenotype, and Reference. See below for descriptions of each column. Additional information relevant to the experiment or interaction is collected and displayed when a corresponding 'i' is selected. At the upper right of the table, the "Filter" box allows you to type any text in order to display in the table only the rows containing that text. Each column header contains up and down arrows that allow you to sort the table by that column in ascending or descending order. At the bottom of the table, you can choose how many records to display in the table, or choose which pages of the table to view. The Download link at the bottom of the table allows you to download its entire contents as a text file. If you have filtered the table, the Download link creates a file containing only the rows that meet your filtering criteria.
Detailed information about each column are below:
|Additional information||The 'i' before the Interactor column contains details about the experiment or additional information that may be useful in interpretation of the interaction. Click on the 'i' to display this information.|
|Interactor||Standard gene name, when available, for protein or gene that was identified in the physical or genetic interaction assay; hyperlinked to that Locus Summary page.|
|Type||Indicates whether the interaction is physical or genetic.|
|Assay||Type of assay used to identify the physical or genetic interaction. Ex. two-hybrid analysis, affinity precipitation, affinity chromatography, dosage rescue, synthetic interaction.|
|Description||First part of the description that is listed on the Locus Summary page for the interacting protein or gene.|
|Annotation||Indicates whether an interaction was manually curated from the literature or added as part of a high-throughput dataset.|
|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.|
|Modification||Any post-translational modification that occurs during an interaction, rather than as a pre-requirement for that interaction.|
|Phenotype||Phenotype that results from the genetic interaction: inviability, slow growth, etc.|
|Reference||Published citation from which the interaction was curated. Citations are linked to the SGD Reference page.|
Interactions between genes are displayed as a network diagram. This diagram can be filtered to display only physical or genetic interactions. The number of interactions displayed can also be changed by filtering by the number of experiments that support an interaction between two genes. This diagram can be downloaded as a PNG file using the 'Download' button at the bottom of the network diagram
At the bottom of the page, the 'Resources' section provides options for looking at genetic and physical interaction data at several different sites, external to SGD. Where possible, links lead to locus-specific information contained in other databases.
Physical and genetic interaction data in SGD may be browsed and searched via several avenues:
- Locus Summary: Locus-specific summary of interactions by assay type are displayed on the Locus Summary page for each gene or feature; the Interaction tab leads to a page containing all physical and genetic interactions curated for that gene.
- YeastMine allows retrieval of chromosomal features using multiple criteria, including interaction data and other custom queries.
- SGD Downloads Site: A file containing interaction data for all genes, 'interaction_data.tab', is available for download.