SGD Help: Genome Snapshot

Contents

  1. Description
  2. Graphical View of the Protein Coding Genes
  3. Genome Inventory
  4. Summary of GO annotations
  5. Distribution of Gene Products by Process, Function and Component
  6. Accessing the Genome Snapshot
  7. Other Relevant Links

Description

This resource provides information on the status of the Saccharomyces cerevisiae genome. It includes information on the genomic features and GO annotations. All the data displayed on this page are available in one or more files (SGD_features.tab, gene_associations.sgd, go_slim_mapping.tab) at SGD's Download site. YeastMine can also be used to retrieve chromosomal features that match specific criteria.

Graphical View of the Protein Coding Genes

A pie chart shows the breakdown of the number of Verified, Uncharacterized and Dubious protein coding ORFs in the S. cerevisiae genome. ORFs are classified as "Verified", "Uncharacterized", or "Dubious" by SGD according to the degree of certainty that each ORF actually encodes a protein.

Genome Inventory

The Genome Inventory table provides a count of each feature type in the genome and in each chromosome. Definitions for each feature type can be found in the Glossary. In addition, the table lists the size of the genome and of each chromosome. This table is updated daily. Clicking on any of the feature types will provide a complete list of that feature type along with their coordinates and other details like gene names and description.

Summary of GO annotations

This summary table provides the current total number of S. cerevisiae gene products (protein and RNA gene products) that have been annotated to one or more terms in each GO aspect (Biological Process, Molecular Function and Cellular Component). Please note that these counts do not include the GO annotations made for ORFs classified as "Dubious", or for features of type "Pseudogene", "Not in S288C" or "Not physically mapped". Also note that the number of annotations displayed in the "Total Number of Annotations" column does not include annotations to the three terms representing lack of knowledge at this time, i.e. "molecular_function unknown", "biological_process unknown", or "cellular_component unknown". The gene_associations file available at SGD's Download site provides the GO annotations for S. cerevisiaegene products.

Distribution of Gene Products by Process, Function and Component

This section provides three bar graphs that represent the GO annotation status of the entire genome using the yeast GO-Slim (a high-level subset of Gene Ontology terms that allows grouping of genes into broad categories such as "DNA replication", "protein kinase activity", or "nucleus") tailored to yeast biology. GO-Slim terms representing broad categories from a single aspect are listed for each graph, along with the percentage of S. cerevisiae gene products annotated to a specific term that maps up the ontology to the GO-Slim term. The complete mapping approach, which maps features to all available GO Slim terms, is used to generate the bar graphs. Only the distribution of "known" Molecular Functions, Biological Processes, and Cellular Components are included in these graphs; annotations to "unknown" are excluded. More information on GO and GO-Slim can be found in SGD's GO help page. To obtain the GO data summarized in these graphs, please contact SGD curators. This data is also available in the go_slim_mapping.tab file, on SGD's Download site. The bar graphs are generated once a day.

Accessing the Genome Snapshot

The Genome Snapshot can be accessed via the Reference Genome option on the Sequence pull down menu in the toolbar at the top of SGD pages.

Go to the Genome Snapshot