- Genome Status
Fission Yeast GO slim terms
"GO slims" are subsets of the Gene Ontology (GO) that provide a broad overview of annotation distribution. Slims can offer a useful overview of a genome or the results of a large-scale experiment. For more information on GO slims, please see the GO Slim Guide at the Gene Ontology website.
The GO slim term set constructed for fission yeast, shown below, provides almost complete coverage of gene products annotated to biological process terms. This slim set is a good starting point for users who wish to identify terms of biological interest to create a "custom slim", or to become familiar with the genome contents.
In the table below, GO IDs link to the QuickGO browser, where you can explore the ontology and annotations further. The annotation totals link to gene lists.
Note that in PomBase, GO annotations are not propagated over the "regulates" relationships by default. This makes it possible to distinguish gene products which are involved directly in a biological process from those which regulate the process: the former will be annotated to a GO biological process term, and the latter will be annotated to a GO term for regulation of the process. Any gene products that are involved both directly in a process and in the regulation of the process will be annotated to both terms. For example, "transcription, DNA-dependent" (GO:0006351) includes all of the core transcription machinery, whereas "regulation of transcription, DNA-dependent" (GO:0006355) includes sequence-specific regulatory transcription factors.
The S. pombe GO slim data now display two annotation totals for each term. One total counts only annotations to the slim term and its is_a or part_of children, excluding regulates relationships; the other includes the regulates children. Most GO slimming applications will present data equivalent to the "including regulates links" column by default.
GO Slim Terms and Annotations
|Name||Term||Current annotations (2013-03-06)|
|Excluding Regulates Links||Including Regulates Links|
|carbohydrate metabolic process||GO:0005975|
|cell wall organization or biogenesis||GO:0071554|
|cellular amino acid metabolic process||GO:0006520|
|cofactor metabolic process||GO:0051186|
|conjugation with cellular fusion||GO:0000747|
|establishment or maintenance of cell polarity||GO:0007163|
|generation of precursor metabolites and energy||GO:0006091|
|lipid metabolic process||GO:0006629|
|mRNA metabolic process||GO:0016071|
|nitrogen cycle metabolic process||GO:0071941|
|nucleobase-containing small molecule metabolic process||GO:0055086|
|protein catabolic process||GO:0030163|
|protein complex assembly||GO:0006461|
|protein modification by small protein conjugation or removal||GO:0070647|
|regulation of mitotic cell cycle||GO:0007346|
|regulation of transcription, DNA-dependent||GO:0006355|
|tRNA metabolic process||GO:0006399|
|vitamin metabolic process||GO:0006766|