Download TAIR Gene Ontology (GO) Annotations

TAIR Gene Ontology (GO) Annotations
This brief tutorial describes how to access and
understand Gene Ontology annotations in
TAIR.
The Gene Ontology is a set of controlled vocabularies used to describe three
qualities of gene products:
• Biological process:
pathways and larger processes made up of the activities of multiple gene
products.
• Molecular function:
molecular activities of gene products
• Cellular component:
where gene products are active
Using gene ontologies allows us to describe gene function in a way that makes it
easier to find and manipulate and analyze computationally. GO also facilitates
interoperability because it is the standard used by all sorts of MODS and genome
databases.
GO annotations are structured associations between gene products that are
machine and human readable. They consist of
• A gene product (the thing being annotated)
• A GO term (function, process or component)
• An evidence ‘code’
• A reference for the evidence
Evidence codes are short (usually 3 letter codes) that indicate the type of
evidence used to support the annotation.
•
•
Experimental Methods
o IDA: Inferred from Direct Assay
o IGI: Inferred from Genetic Interaction /IGI)
Non-experimental Methods (e.g. computational analysis)
o RCA: Reviewed Computational Analysis
o ISS: Inferred from Structural Similarity
What can you do with TAIR GO annotations?
•
•
•
•
•
View all GO annotations for a given locus
Search for sets of genes by GO terms
Browse the ontologies and find annotations
Download GO annotations for a set of genes or the whole genome
GO term enrichment using external tools (AMIGO)
The locus page shows all of the annotations associated the gene product,
grouped according to type.
Click on the annotation detail to view a list of all the annotations.
Here you can view the essential details of each annotation.
•
•
Click on the reference link to find the paper in which the experiments are
described.
Or, you want to find similarly annotated genes, you can click on the GO
term itself to view the term details and see other genes anntotated to the
same term.
IN TAIR, you can find genes by GO term in the gene search. Enter in a term. The
default search returns all annotations. If you prefer, you can limit the results to
only those genes annotated based on experimental evidence.
You can also search and browse the ontologies directly by selecting
“Ontologies/Keywords” under the Browse menu.
You can search for a specific term and then use the tree viewer (click “treeview”)
to explore the ontologies. You can choose which types of associated data to
display, including annotations, genes or papers.
If you have a set of genes that you want to obtain GO Annotations for, you can
use the GO Annotation search tool. For example, if you have a list of members of
a gene family or co-expressed genes, you can enter the list and download all of
the annotations for that gene set.
You can also view the results as broader functional categories and display that
either as a list or in pie/bar chart formats. You can do this for the whole genome
as well as your subset of genes.
If you want to do term enrichment to find GO terms that are over represented in a
dataset, you can use the Term Enrichment Tool available from the Gene
Ontology consortium.
TAIR’s annotations are sent to the GO consortium monthly, so you will be
accessing the most recent GO annotations from TAIR. Upload your list of locus
identifiers and choose A. thaliana as the dataset, and set your set your
parameters. For example you may want to restrict your results to only those gene
function annotations that are experimentally based, or compare to the whole
dataset.
We encourage you to learn more about the gene ontologies by visiting the GO
website. If you have questions or comments, please email us at
[email protected].
For more information about the gene ontologies please visit the Gene Ontology
website http://www.Geneontology.org.