SGD Help: Locus Summary Page

The Locus Summary page represents the focal point for information about all chromosomal features in the Saccharomyces cerevisiae genome. This includes information about the gene, and the encoded RNA and protein, as well as structural features. This information is constantly being updated as new literature, datasets and external links become available. Efforts are also being made to reference all information presented on the locus page. What follows is a description of the informational content presented on the locus page.

Contents

  1. Overall Organization of the Locus Summary Page
  2. Section-by-Section Guide to the Locus Summary Page
    1. Basic Information
    2. Gene Ontology Annotations
    3. Pathways
    4. Mutant Phenotypes
    5. Interactions
    6. Expression Summary
    7. Regulation
    8. Protein Information
    9. Sequence Information
    10. Analyze Sequence
    11. Resources
    12. Summary Paragraph
    13. References Cited on This Page
  3. Additional Information on the Locus Summary Page

Overall Organization of the Locus Summary Page

There are two main aspects to the overall organization of each SGD locus page.

  • Sections - Each page is divided into several sections, described in more detail below, that are separated by gray bars. The presence of a few sections depends upon the type of chromosomal feature described on the page; for example, an ORF page (such as SIR2) will contain all of the sections described below, while a page for a centromere (e.g. CEN1) will only contain sections pertinent to DNA.
  • Tabs - At the top of the page is a series of tabs; clicking on each tab takes you to a page with more information and data pertaining to that topic, for that gene. The pages linked from the tabs Gene Ontology, Phenotype, Interactions, and Protein are also accessible from the links on the right side of the respective gray section dividers.

Section-by-Section Guide to the Locus Summary Page

For easy navigation, the Locus Page is organized into several sections that allow similar types of data to be grouped and viewed together. Many of these sections also contain relevant links to external resources.

Basic Information

This section lists the standard locus name, the systematic name, aliases, retired gene names, and also indicates whether a name is standard or reserved. It addition, it includes the following information:

  • Feature Type - indicates what feature type resides on this chromosomal sequence. Feature types include: ORF, rRNA, snRNA, snoRNA, tRNA, ncRNA, telomeres and associated subfeatures (telomeric repeat, X element combinatorial repeats, X element core sequence, Y' element), centromere, ARS elements, retrotransposon, LTR, transposable element gene (TyORF), pseudogene, as well as features that are "not in the systematic sequence of S288C" and those that are "not physically mapped". ORF's receive additional designations of either "Dubious", "Uncharacterized", or "Verified" depending the degree of certainty that they actually encode proteins. Please see the Glossary for explanations of these terms.
  • Description - contains a concise summary of the function and biological role of each gene product. In cases where function and role isn't known, the key published information is included in the Description. Descriptions have a 480-character limit, allowing for the inclusion of a large amount of information, and are replacing Gene Summary Paragraphs (see below) as a source of up-to-date information in a free-text format.
  • Name Description - contains the expanded form of the standard name, as described in the literature.
  • Chromosomal Location - shows chromosomal coordinates and, when applicable, genetic position. Links to the Chromosomal Features Map of that chromosomal region and the genome browser GBrowse are provided; these links take you to an expanded view of this region of the genome so that the feature of interest can be viewed in the context of its chromosomal surroundings.

Gene Ontology Annotations

The Gene Ontology (GO) Annotations (Molecular Function, Biological Process, and Cellular Component) describe a gene's molecular function(s), its broad role in biological processes, and its presence in subcellular locations, structures or macromolecular complexes. Each annotation links to a page that defines the term and shows all yeast genes annotated to that term. In addition, the type of evidence (evidence code) used by the curator to assign the GO term is indicated in parentheses and is linked to an explanation of that evidence code. Clicking either on the GO tab at the top of the Locus Page or on the "GO evidence and references" link in the gray bar takes you to an expanded display of the GO annotations, including references. The GO annotations use a controlled vocabulary that allows powerful searches within SGD and across other databases. For more information about GO at SGD, please see the SGD help page for GO.

Pathways

The Pathways section appears on the Locus Summary page only for genes involved in metabolic pathways. The section lists all of the pathways in which the gene product functions. The names of the pathways are linked to graphical displays, which were created using the Pathway tools software developed by Peter Karp and his associates at SRI. See the Pathway tutorials for more information.

Mutant Phenotypes

SGD uses a controlled vocabulary to curate mutant phenotype data. Moreover, we collect data from large-scale survey studies as well as classical genetic experiments. The Mutant Phenotype section lists the phenotype(s) of different types of mutations. Details about the experiments and associated phenotypes, as well as references, are displayed as a table accessible from the Phenotype tab or by clicking on the "Phenotype evidence and references" link in the gray bar. For more information about the phenotype data in SGD, see the phenotype help page.

Interactions

Physical and genetic interaction data are currently bulk loaded from the BioGRID database hosted by Mike Tyers' group at University of Toronto. The curation of the BioGRID interaction data is a collaborative effort between the Tyers lab, SGD Colony at Princeton University and SGD project at Stanford. Details about the experiments and associated interactions, as well as references, are displayed in a sortable table accessible from the Interactions tab or by clicking on the "Interaction evidence and references" link in the gray bar. More information about physical and genetic interaction data is available on the interactions help page.

Expression Summary

The Expression Summary section shows a summary graph displaying the number of experiments in which mRNA expression changed, either increasing or decreasing, and the extent of the change. Clicking on this graph takes you to an entry page to access the microarray analysis tool SPELL, which allows you to find the datasets that show relevant changes in gene expression for a gene or gene list. For more information about SPELL, view a brief video tutorial. The Expression Summary section also contains a number of external links to resources with expression information.

Regulation

The Regulation section is currently present only on Locus Summary pages for a set of 147 transcription factors (TFs) that bind DNA directly (retrieve list of TFs). It presents the consensus binding site sequence(s) for that TF as determined in several high-throughput studies, along with links to search intergenic regions for those sequences using SGD's Pattern Matching tool. It also summarizes the numbers of target genes of that TF and regulators of that TF. Details are displayed on the Regulation tab page, which can be accessed via the Regulation tab at the top of the Locus Summary page or via the "Regulation evidence and references" link in the regulation section of the Locus Summary page. For more information, see the Regulation Help documentation.

Protein Information

The protein information section contains links to a number of resources, particularly those with localization and homolog information. In addition, the "Protein evidence and references" link in the gray section divider takes you to the first page of a trio of pages containing protein-specific information. These pages can also be accessed via the Protein tab. These three pages contain information about the protein's sequence, chemical and physical properties, and domains and motifs. The protein is also displayed in an interactive proteome viewer that highlights sequence information. See the protein information help page for more details.

Sequence Information

This section repeats some of the chromosomal information and links presented earlier on the page (see Basic Information above). In addition, this section displays dates of most recent sequence-related updates, details of subfeatures, and options to retrieve sequence data from a variety of S. cerevisiae strains. There are two types of dates in the "Last Update" section:

  • Coordinates - indicates the date when the chromosomal coordinates of the feature were last changed.
  • Sequence - indicates the date when the sequence of the feature was last changed. This can be due to a sequence change within the feature, a change in the intron/exon structure of the feature or an extension or deletion of the feature at either the 5' or 3' end.

Analyze Sequence

This section provides links to sequence analysis tools and information, both within and external to SGD, that allow you to perform comparison analyses between the S288C gene and that of other strains and species.

Resources

The Resources section displays the SGDID for the chromosomal feature, and a link to the All Associated Sequences page. This page is a compendium of all S. cerevisiae sequence entries for any allele or strain found in various external databases. See the All Associated Sequences help page for more information.

Summary Paragraph

The Gene Summary Paragraph provides a summary of published biological information for a gene and its product that is designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus. However, as of 2012 SGD curators will no longer write summary paragraphs. Instead, we have increased the length of the Description lines in order to provide more up-to-date information.

References Cited on This Page

This section lists the references used to curate information displayed in the Standard Name, Alias, Description, Name Description, and Summary Paragraph fields. Note that this section is not a comprehensive listing of publications relevant to this gene. To retrieve a list of all publications annotated to this gene, click on the Literature tab at the top of the page.