SGD Help: Expression Data

View a quick video tutorial about the Expression pages in SGD.

The Expression page presents detailed information about the expression of a particular gene product, along with references for each observation. It is accessible from the Expression section of the Locus Summary, where the data are presented in summary form, and also from the Expression tab at the top of the Locus Summary. Data are presented in multiple ways - a histogram, tabular table, and a network diagram of genes with similar expression profiles as the gene of interest, across all microarray datasets in our database.

All datasets relevant to the gene of interest may be downloaded as a tab-delimited text file by clicking the 'Download' button near the bottom of the 'Annotations' table. Individual datasets can be downloaded by clicking through to the dataset page and using the 'Download' link at the bottom of the page.

Contents

  1. Expression data
  2. The Expression page
    1. Expression overview
    2. Annotations
    3. Similar Expression Profiles
    4. Resources
  3. Searching and browsing expression data

Expression data

Expression data are primarily derived from records deposited in the Gene Expression Omnibus (GEO). Dual channel data are typically loaded as log2 ratios of the experimental condition relative to the control, while data from single channel arrays are normalized using the average expression for each gene across all conditions. PCL files are generated and used to populate SPELL (Serial Pattern of Expression Levels Locator), a query-driven search engine for large gene expression microarray compendia where informative datasets for a small set of query genes can readily be identified. A small fraction of these datasets were manually curated before a pipeline for retrieval from GEO was created, and may not be stored in GEO.

The Expression page

Context-Specific Information and Help

Please note that context-specific information and help can be found on the Expression page itself, connected directly with specific data sections on that page. Just click on the information icon to pop-up short descriptions of the data or the help icon for help in using the table, graph, or visualization displaying the data.

Expression overview

An overview of expression data is presented in the form of a histogram to graphically represent the distribution of data from the large number of available microarrays. The data in the histogram represents log2 ratios (X-axis) that have been grouped into ranges and plotted against the number of conditions (Y-Axis) that satisfy the grouped ratio. The histogram by default is presented with the Y-axis values in log10 space to better visualize the large amount of data, and enhance the tails at either expression extreme. The toggle slider can be switched to view the data in linear space where the tails are less obvious.  Based on the length of the tails at the expression extremes, the size of the upper and lower range groupings has been increased, and highlighted with bright colors.  The histogram is dynamic and clicking on any of the bars results in filtering of the data presented in the annotation table (below) to provide insight into the datasets in which the expression is altered by a given amount. The default view can be regenerated by either reloading the page or deleting the text in the filter box present at the top of the annotation table.

Annotations

The Annotations table contains the following columns: Dataset, Description, Categories, Number of Conditions, and Reference. Descriptions of the columns are available in the table below. 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.

Dataset A link to the dataset represented in the histogram and contained within SPELL.
Description A short description of the experimental focus of the data presented in the dataset.  
Categories Controlled vocabulary terms assigned based on the area(s) of biology investigated; used in SPELL to group and filter like data; linked to a page that summarizes all datasets with a category term.
Number of Conditions Number of unique experimental conditions: including mutant backgrounds, growth conditions, chemical perturbations and/or time, dose-response analyses represented in the dataset.
Reference Published citation for the expressions data. Citations are linked to the SGD Reference page.

Similar Expression Profiles

Genes with expression profiles across all stored microarray experiments that are similar to the gene of interest, are displayed as a network diagram. The gene network can be filtered by changing the number of datasets that show highly correlated expression 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 expression data at several different sites. With the exception of SPELL, these sites are external to SGD. Where possible, links lead to information contained in other databases specific to the gene of interest.

Browsing and searching expression data

Expression data in SGD may be browsed and searched via several different ways:

  • Locus Summary: A locus-specific summary of expression data is displayed on the Locus Summary page in the form of a histogram for each gene or feature; clicking on the diagram takes you to the same page as the expression tab.
  • SPELL: Links to SPELL can be found on Locus Summary pages and on the tabbed Expression pages. 
  • YeastMine: allows retrieval of expression data based on the author, PubMed ID or dataset name, or the retrieval of expression data for a specific gene.
  • SGD Downloads Site: Files containing expression data for experiments used to populate SPELL are available for download.