Princeton University
Lewis-Sigler Institute for Integrative Genomics

HELP: GENERIC GENE ONTOLOGY (GO) TERM MAPPER

Our GO Tools: Generic GO Term Finder | Generic GO Term Mapper


Contents


Description: The GO Slim Term Mapper Help Page at SGD gives the following description of the GO Slims :
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: biological process, molecular function, 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.

This GO Term Mapper tool maps the granular GO annotations for genes in a list to a set of broader, high-level parent GO slim terms, allowing you to bin your genes into broad categories. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent GO slim terms. For a better view of parent:children relationships of GO terms, please visit the AMIGO web site.

This GO Term Mapper tool serves a different function than the GO Term Finder tool. The GO Term Mapper tool simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, the GO Term Finder tool finds the GO terms significantly enriched in a submitted list of genes.




Please send comments or questions to gotools@genomics.princeton.edu
.