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 also be viewed using AMIGO.
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 Mapper tool at AspGD uses the GO Slim terms picked by the AspGD curators based on annotation statistics and biological significance. The Aspergillus GO Slim may be downloaded from AspGD's Download Data page.
The GO Slim Mapper tool at AspGD 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 (ie. GO Slim) terms.
For more information on GO in general, visit the Gene Ontology website or the GO help page provided by the Saccharomyces Genome Database (SGD).
Note that the default sets of annotations used by GO Slim Mapper are analogous in AspGD and in the Candida Genome Database (CGD), but different from the set used at the Saccharomyces Genome Database, SGD. In AspGD and CGD, all GO annotations (Manually curated, High-throughput, and Computational) are used as the default set, while in SGD Computational annotations are excluded from the default set. Computational annotations are included for AspGD and CGD because they augment the GO annotation coverage of the genomes, providing annotation for many uncharacterized genes. In contrast, in SGD the greater extent of characterization of S. cerevisiae genes means that computational annotations are frequently redundant with or less specific than experimentally-derived annotations, and dilute this higher-quality set.
You can also download the results into a tab-delimited (ie. excel readable) file by clicking on the Download Results link.
|Gene Name||Molecular Function Annotation|
|PHO1||hydrogen-transporting two-sector ATPase|
|GO-Slim term||Cluster frequency||Genes annotated to the term|
|Function: transcription regulator||2 out of 4 genes, 50%||PHO2, PHO4|
|Function: enzyme||2 out of 4 genes, 50%||ATP6/PHO1, PHO3|
|Function: transporter||1 out of 4 genes, 25%||ATP6/PHO1|
|Function: molecular_function unknown||0 out of 4 genes, 0%||none|
|Function: structural molecule||0 out of 4 genes, 0%||none|
|Return to AspGD||Send a Message to the AspGD Curators|
AspGD Copyright © 2008-2013 The Board of Trustees, Leland Stanford Junior University, and Broad Institute.
Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
To cite AspGD, please use the following reference: Cerqueira GC, Arnaud MB, Inglis DO, Skrzypek MS, Binkley G, Simison M, Miyasato SR, Binkley J, Orvis J, Shah P, Wymore F, Sherlock G, Wortman JR (2013). The Aspergillus Genome Database (AspGD): multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 42(Database issue):D705-D710; see How to cite AspGD.