SGD Help: Physical and Genetic Interactions

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, and also from the Interactions tab at the top of the Locus Summary. Data are presented in tabular form. The table is sortable and searchable. More information is available on how to use the table. All data may be downloaded as a tab-delimited text files by clicking the 'Download Unfiltered Data' link near the 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.

Contents

  1. Physical and genetic interaction data
  2. Further analyzing interaction data
  3. Using the Table
    1. Table options
    2. Filtering
    3. Sorting
    4. Table settings

Physical and genetic interaction data

Physical and genetic interaction data are presented in a table that contains the following columns:

Feature Feature name of the protein or gene that was identified in the physical or genetic interaction assay; hyperlinked to the Locus Summary.
Gene Standard gene name, when available, for protein or gene that was identified in the physical or genetic interaction assay; hyperlinked to that Locus Summary.
Description First part of the description that is listed on the Locus Summary page for the interacting protein or gene.
Experiment Type Type of physical or genetic interaction. Ex. two-hybrid analysis, affinity precipitation, affinity chromatography, dosage rescue, synthetic interaction.
Type Indicates whether the interaction is physical or genetic.
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 All of the physical and genetic interactions listed in SGD 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.
Modification Any post-translational modification that occurs during an interaction, not that a previously modified protein is involved in an interaction.
Phenotype Phenotype that results from the genetic interaction: inviability, slow growth, etc.
Note Details about the experiment or additional information that may be useful in interpretation of the interaction.
Reference Published citation from which the interaction was curated.

Further analyzing interaction 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.

  • GO Term Finder uses a list of genes to find 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.
  • SPELL is a tool that searches data from published expression studies to find and compare expression levels for your genes of interest. When multiple genes are provided as a query, SPELL determines the relevance of each dataset to that query based on the level of co-expression within each dataset. Additional genes are then identified given these dataset relevances.
  • Clicking the 'Download Unfiltered Data' link will download data for the entire gene list in a tab-delimited file.
  • Clicking the 'Download options' link will send the gene list to YeastMine for further download options including Sequence, Coordinates, GO annotation, Interactions, Phenotypes, etc. Note that pop-up windows must be enabled for the export to work correctly.

Using the Table

Table options

Double click on any table cell to display a menu that includes additional options to manage the data being displayed in the table. Pop-up blockers must be turned off for export options to be functional.

  • Sort by [column name]: sorts the data in the table based on the column listed in the menu. Behaves the same as sorting using the column header.
  • Filter by [column name]: provides options to view a subset of the data by including or excluding the data shown in a table cell or by filtering the data based on a keyword.
  • Print/Export: creates an HTML page of the data displayed in the table. Useful for printing pages. Pop-up blockers must be turned off.
  • Hide/Show: provides an option to hide a column from the table or to display a previously hidden column from the table view.

Filtering

  • Enter any phrase into the search box located below the column header. If there are no results, try appending a wildcard character (*) before or after the word (such as phosph* or *phosph). An icon of a funnel will appear next to the column heading to indicate which column is being used for the filtering.
  • To view all the data, all filters need to be removed. An option to remove all filters is available at the top of the table. Alternatively, double-click on a table cell and select the Filter by option on the pop-up menu.

Sorting

Click on the column header to sort that column. An upwards facing arrow indicates the data were sorted from A-Z or 0-9. A downwards facing arrow indicated the data were sorted Z-A or 9-0.

Table settings

  • The width of the table columns can be adjusted by dragging the column border in the heading.
  • The table only displays as much data as will fit in the browser window. Use the scroll bar located to the right of the table to view additional rows of data.
  • Scrolling to the end of the page and resizing the browser window will add additional rows to the sortable table.

Go to Interactions