SGD Help: Regulation

The Regulation page summarizes the regulatory context of transcription factors (TFs) that bind DNA directly. This page is accessible from Locus Summary pages for this set of TFs (retrieve list of TFs) by clicking either the "Regulation" tab or the "Regulation evidence and references" link in the Regulation section.

Contents

  1. Contents of the Regulation Page
    1. Regulation Summary
    2. Tables on the Regulation Page
    3. Domains and Classification
    4. Binding Site Motifs
    5. Regulatory Targets
    6. Shared GO Processes
    7. Regulators
  2. Analyzing and Downloading Regulation Data
    1. Downloading Data from Tables on the Regulation Page
    2. Retrieving Regulation Data from YeastMine
  3. Citing Regulation Data

 

Contents of the Regulation Page

Regulation Summary

The Regulation Summary is a free-text paragraph written by SGD biocurators. It is meant to give a capsule summary of the place of that TF in the regulatory network. The paragraph may include the classification of the TF, its target genes and processes, and information about the regulation of expression and activity of the TF itself. The citations for this paragraph are not intended to be comprehensive, and review articles are cited wherever possible.

Gene names in the Regulation Summary are linked to their SGD Locus Summary pages. Reference citations are linked to their SGD Paper pages.

Tables on the Regulation Page

All tables on the Regulation page may be sorted and filtered. Click on any column header to sort that column. Type any text into the "Filter:" box to view rows of the table that contain that text. The "Display:" pull-down lets you choose the number of rows to view, from 10 - 100.

Domains and Classification

The Domains and Classification section displays the results of an InterProScan using the protein sequence of the TF to query for domains and motifs from several databases. The coordinates of each domain are shown, along with the accession ID, description of the domain, and the source of the domain information. The domain accession ID is linked to the entry for that domain in its parent database.

This table also displays the Class and Family membership of the TF, as defined by the JASPAR database. The accession ID is linked to the summary page for that TF in the JASPAR database.

Binding Site Motifs

The Binding Site Motifs section displays high-confidence binding site sequence motif(s) for the TF, from the YeTFaSCo database. In the sequence logo, the height of the letter representing a nucleotide is proportional to the frequency with which that nucleotide occurs at that position. Each of the four nucleotides is represented using a different color. Each logo image is linked its YeTFaSCo record.

The "View predicted binding sites in GBrowse" link leads to a GBrowse search for all predicted binding sites for the TF, including multiple motifs if there is more than one high-confidence binding motif. From the search results page you can navigate to a graphical view of the genomic regions containing predicted binding sites.

Regulatory Targets

Data in the Regulatory Targets table represent targets of the TF as determined by various experimental methods. Evidence codes were mapped to the Evidence Code Ontology (ECO).

Columns in the Regulatory Targets table currently include:

Target Gene name of the target gene (or systematic name if no gene name assigned), linked to its Locus Summary page
Experiment type of experiment supporting the regulator-target relationship (ECO term name)
Assay type of assay supporting the regulator-target relationship
Construct type of construct used in the assay
Conditions conditions used in the assay
Strain background strain background used in the assay
Reference citation for the paper in which the evidence was published, linked to its SGD Paper page

Shared GO Processes

The Shared GO Processes table displays an analysis of the target genes from the Regulatory Targets table using the Gene Ontology Enrichment widget from YeastMine. The widget compares the Biological Process annotations of the target genes and displays GO terms that are significantly shared among that set of genes. The Holm-Bonferroni test correction is used in the calculation, and shared terms with a maximum p-value of 0.05 are displayed. These terms reflect the biological processes that are regulated by this TF.

Regulators

The Regulators table draws from the same pool of data that are displayed in the Regulatory Targets table, but displays regulator-target relationships where the TF of the page is the target of regulation. Columns in the table are the same as in the Regulatory Targets table, except that the gene shown is the regulator of the TF.

Analyzing and Downloading Regulation Data

Downloading Data from Tables on the Regulation Page

Above the left-hand side of each table on the Regulation page is a box presenting four options for downloading the data from that table:

Copy copies the table data to the clipboard
CSV downloads the table data in comma-separated values format
PDF downloads the table data in PDF format
Print shows the entire table in a browser window that can be printed (Note: to go back to the Regulation page from this view, press "Escape".)

Retrieving Regulation Data from YeastMine

All of the data displayed on the Regulation page, plus additional data, are available from YeastMine. You can search for and download data, or create gene lists and analyze them further using additional YeastMine queries.

YeastMine templates (pre-composed queries) for regulation data include:

Retrieve all Regulators and their Summary Paragraphs Retrieve the list of all regulator genes that have Regulation Summary paragraphs, along with the paragraph text and references.
Gene (regulator) --> Gene (targets) Start with the gene name or systematic name of a regulatory gene and retrieve its target genes, along with evidence (ECO term name and ID), reference, and source. For some targets, data on experimental condition, direction of regulation (activated or repressed), p-value, or false discovery rate are also available. You can also run this query using a list of regulatory genes.
Gene --> Regulation Summary + References Start with the gene name or systematic name of a regulatory gene and retrieve its Regulation Summary paragraph and references for the paragraph. You can also run this query using a list of regulatory genes.
Gene --> PWM-predicted binding sites Start with the gene name or systematic name of a regulatory gene and retrieve the number of binding sites that are predicted in the genome, either between genes or within genes. Numbers predicted at three different p-values are shown. You can also run this query using a list of regulatory genes.
Gene (target) --> Gene (regulators) Start with the gene name or systematic name of a target gene and retrieve its regulators, along with evidence (ECO term name and ID), reference, and source. For some targets, data on experimental condition, direction of regulation (activated or repressed), p-value, or false discovery rate are also available. You can also run this query using a list of target genes.
JASPAR Class --> Genes Select the name of a transcription factor class, as defined by the JASPAR database, from the pull-down menu and retrieve all of the S. cerevisiae transcription factors in that class.
JASPAR Family --> Genes Select the name of a transcription factor family, as defined by the JASPAR database, from the pull-down menu and retrieve all of the S. cerevisiae transcription factors in that family.

Citing Regulation Data

To cite the regulation data viewed on or downloaded from SGD Regulation pages or from YeastMine, please see instructions here.