SGD Help: Physical and Genetic Interactions

View some quick video tutorials about the Interactions pages in SGD: Interactions Overview | Interaction Network

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.

Contents

  1. Interaction data
  2. The Interactions page
    1. Interactions overview
    2. Annotations
    3. Interaction Network
    4. Resources
  3. Searching and browsing interaction data

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 Interactions page

Interactions overview

View a quick video tutorial about the Overview section of the Interactions page.

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.

Annotations

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:

Interaction network

View a quick video tutorial about the Network diagrams on the Interactions pages.

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

Resources

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.

Browsing and searching interaction data

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.