SGD Help: GO Slim Mapper

Contents

• Background and Description
• Query Page
• Results
• Example
• Complete Mapping of GO slim terms
• Associated Glossary Terms
• Useful Links

Background and Description

The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. A gene product's biology is represented by three ontologies: molecular function, biological process and cellular component. The use of a consistent vocabulary allows genes from different species to be compared based on their GO annotations. To provide the most detailed information available, gene products are annotated to the most granular GO term(s) possible. For example, if a gene product is localized to the perinuclear space, it will be annotated to that specific term only and not the parent term nucleus. In this example the term perinuclear space is a child of nucleus. Parent-children relationships can be viewed better using AMIGO Tree View.

However, for many purposes, such as reporting the results of GO annotation of a genome, analyzing the results of microarray expression data, or cDNA collection, it is very useful to have a high level view of the three ontologies. For example, if you wanted to find all the genes in an expression cluster that were localized to the nucleus, it would be useful to be able to map the granular annotations, such as perinuclear space, to general terms, like nucleus. Thus, GO slim was created. GO slim is a high level view of GO: a slice of the broad, high level terms such as DNA replication, transcription, and transport. There are several versions of GO slims created for different genomes and the GO slim terms are updated periodically. To view and/or download other GO slims, go to the GO slim ftp site. The GO slim tool at SGD uses the GO slim terms picked by the SGD curators based on annotation statistics and biological significance.

The GO Slim Mapper at SGD was created to allow you to map the granular annotations of the query set of genes to one or more high level, parent GO Slim terms. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent (i.e., GO slim) terms.

For more information on GO in general, visit the Gene Ontology website or the GO help page at SGD.

Query Page

• Step 1: Enter your gene(s)

  You can either type the names of the genes in the input box or upload a file that contains the gene names. Note that the program requires more time to process a long list (greater than 100 genes) than a short list.

• Step 2: Choose your GO Slim Set:
  

  Three GO Slim Sets are available at SGD.

  1. Macromolecular complex terms: Component: A set of granular protein complex terms from the cellular component ontology, useful for determining whether your protein of interest is a member of a particular complex. This set is a list of all protein complex terms and not truly a Slim set.
  2. Super GO-Slim:Process: A small set of very broad, high level GO Biological Process terms, useful for binning groups of genes in general categories.
  3. Super GO-Slim:Function: A small set of very broad, high level GO Molecular Function terms, useful for binning groups of genes in general categories.
  4. Super GO-Slim:Component: A small set of very broad, high level GO Cellular Component terms, useful for binning groups of genes in general categories.
  5. Yeast GO-Slim:Component: A set of high level GO terms that best represent the major biological components that are found in S. cerevisiae. These terms have been selected by SGD curators based on annotation statistics and biological significance.
  6. Yeast GO-Slim: Function: A set of high level GO terms that best represent the major biological functions found in S. cerevisiae. These terms have been selected by SGD curators based on annotation statistics and biological significance.
  7. Yeast GO-Slim: Process: A set of high level GO terms that best represent the major biological processes that are found in S. cerevisiae. These terms have been selected by SGD curators based on annotation statistics and biological significance.
  This tool is designed to search only one of the GO Slim set at a time in order to minimize the search time. When you choose a GO Slim Set, the terms from that set will be listed in the box under Step 3.

• Step 3: Choose your GO Slim terms Select at least one GO slim term from the list. You can also select all the terms in the list. For information about a particular GO Term and its definition, type the GO Term (for example, peptidase activity, bud tip) in the Quick Search box at the top of the page.

• If you click the Search button after Step 3, the tool will map annotations made to your input list of genes by compiling data from both the Manually curated and High-throughput sets. You can go to optional Step 4 to filter by Annotation Method. GO Slim Mapper at SGD queries Manually curated and High-throughput annotations only and does not query annotations obtained using computational methods.

• Step 4: Select Annotation Method(s) This is an optional step that allows you to select either the Manually curated or the High-throughput annotation set rather than both when using GO Slim Mapper to map annotations to your input set of genes.

  Results Page

  The results page displays the number of genes from your input list that were mapped, the reasons why some genes may not have been mapped and a table that displays the mapping results.

  Results Table

  The first column in the table lists the GO slim terms that were chosen in Step 3, the second column lists the frequency with which each GO slim term is associated (directly, or indirectly, via a parental relationship with a granular term) with the genes in your list and the third column lists the genes that were mapped to that GO term. Each gene name is hyperlinked to its locus page, which shows all GO annotations associated with that gene.

  You can also download the results into a tab-delimited (ie. excel readable) file by clicking on the Download Results link.
  
  Note: Occasionally browser-specific problems occur while uploading a file or displaying the results. Please contact us at yeast-curator@genome.stanford.edu if you notice such problems.

  Tips to interpret the results

  If some or all of the genes in your input list are not mapped to a GO Slim term, consider these possible reasons.
  1. Genes in your input list may have been binned into a category called 'cannot be mapped to a GO Slim term'. What does this mean?
     There are some genes whose annotations cannot be mapped to a GO slim term because the GO term used for the annotation does not map to an existing GO slim term. For example, SSB1 is annotated to the cell component 'polysome', but the term 'polysome' does not map up to an existing GO slim term. Hence it gets binned into this category.
  2. Genes in your input list were filtered out by the Annotation filter option in Step 4. For example, if you are trying to map the GO annotations of only the Annotation Method: Manually curated and your input list of genes have annotations of both types (Manually curated and High-throughput), then filtering out Annotation Set 'High-throughput' in Step 4 will remove those genes that have this type of annotation. In this case you will see a message like the one below, on the top of the results page.
     
     The following gene(s) URA7, URA3 cannot be mapped because they have no annotations for the specified GO Slim terms in the selected annotation set Manually curated.

  Example

  Consider a small group of 4 genes: CDC53, PHO2, PHO3 and PHO4. The following are the granular molecular function annotations for these genes in SGD.

  Gene Name	Molecular Function Annotation
  CDC53	ubiquitin-protein ligase activity
  	DNA replication origin binding
  	protein binding, bridging activity
  PHO2	transcription factor activity
  PHO3	acid phosphatase activity
  PHO4	transcription factor activity

  Searching for all the GO slim function terms will map these annotations to the following:
  

  GO-Slim term	Cluster frequency	Genes annotated to the term
  DNA binding	3 out of 4 genes, 75%	CDC53, PHO2, PHO4
  transcription regulator activity	2 out of 4 genes, 50%	PHO2, PHO4
  hydrolase activity	1 out of 4 genes, 25%	PHO3
  ligase activity	1 out of 4 genes, 25%	CDC53
  protein binding, bridging activity	1 out of 4 genes, 25%	CDC53

  From the two tables above the following conclusions can be drawn:

  • The genes CDC53, PHO2 and PHO4 have DNA binding activity, although their granular annotations are to the terms DNA replication origin binding and transcription factor activity.

  • The genes PHO2 and PHO4 function as transcription regulators although their granular annotations are to the term 'transcription factor activity'

  • The terms DNA replication origin binding and transcription factor binding are mapped to the parent term DNA binding activity as shown below.

    DNA binding->
        sequence-specific DNA binding->
              DNA replication origin binding->
        transcription factor activity->

  • This example also shows the existence of multiple parents for the same term. 'transcription factor activity' has two parents- 'DNA binding' and 'transcription regulator activity' as shown below.
    

    DNA binding->
        sequence-specific DNA binding->
              DNA replication origin binding->
        transcription factor activity->

    molecular_function->
        transcription regulator activity->
              transcription factor activity->

  • There are no genes in the input set that have been annotated to the term 'molecular function unknown'.
  You can see the relationships mentioned above and much more using

  Complete Mapping of GO slim terms

  Some GO slim terms are children of other GO-slim terms. For example, "meiosis" is a child of "cell cycle" but both are terms in the GO-slim process ontology. The GO Slim Term Mapper uses a 'complete mapping approach' and maps features to all available GO slim terms, regardless of parentage. This means, for example, that if a feature is annotated to "meiosis," then the GO Slim Term Mapper will also report it as annotated to "cell cycle."

  Data in the go_slim_mapping.tab file on SGD's FTP site and the GO Slim Bar graphs on the Genome Snapshot page are also generated using the 'complete mapping approach'.

  Associated Glossary Terms

  • Parent Term
  • Child Term
  • GO-Slim
  • Tree-View
  • GO Annotation
  • GO Annotation Method
  • Manually curated
  • High-throughput
  • Computational
  • GO Annotation Source

  Other Useful Links

  • GO Term Finder: The GO Term Finder searches for significant shared GO terms, or parents of those GO terms, used to describe the genes in your list to help you discover what the genes may have in common.
  • GO Tutorial: interactive tutorial for using GO in SGD.
  • GO Help Page: general help page for GO in SGD.
  • GO Home Page: home page of the GO consortium.

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