1. Community Annotation of Gene Function with GONUTS Jim Hu EcoliHub/EcoliWiki Dept. of Biochemistry and Biophysics Texas A&M University

2. Overview Why use GO? –What do we mean by function? A wiki approach to using and understanding GO –Browsing and usage –Community annotation –Annotation jamborees

3. Why use GO? Many situations in "genomic" biology that involve looking for properties of lists of genes or gene products –similar expression patterns –found in an interaction network –found in a compartment –found in a mutant hunt –conserved (or not) in evolution The general question: what can these commonalities tell us about function? –First, what are their functions?

4. Gene Ontology (GO) Begun by SGD, Flybase, Mouse Genome Informatics –Now ~16 groups focused on organisms, clades, diseases, UniProt, Reactome Goals –Dynamic controlled vocabulary –Support unification of annotation across tree of life –Improve annotation quality and consistency –Support machine inference Divides function into three ontologies: –Molecular function –Biological process –Cellular component > 28K terms, and growing

5. Cellular Component from GOC

6. Molecular Function activities or “jobs” of a gene product glucose-6-phosphate isomerase activity from GOC

7. Biological Process transcription from GOC

8. GO:0003674 molecular function GO:0003674 molecular function GO:0016740 transferase activity GO:0016740 transferase activity GO:0016772 transferase activity, transferring phosphorus- containing groups GO:0016772 transferase activity, transferring phosphorus- containing groups GO:0016301 kinase activity GO:0016301 kinase activity GO:0016773 phosphotransferase activity, alcohol group as acceptor GO:0016773 phosphotransferase activity, alcohol group as acceptor GO:0003824 catalytic activity GO:0003824 catalytic activity GO:0019200 carbohydrate kinase activity GO:0019200 carbohydrate kinase activity GO:0004335 galactokinase activity GO:0004335 galactokinase activity other phosphotransferase activities with alcohol acceptors other molecular functions other catalytic activities other transferase activities other phosphotransferase activities other kinase activities other carbohydrate kinase activities GO terms are arranged in a DAG

9. Can GO annotation be done by the community curation? GO annotation = associating gene products with GO terms, references, and evidence –Finding the right GO term –Understanding the relationships across the DAG –Understanding evidence codes –Best practices –etc. Go to live demo here GONUTs (http://gowiki.tamu.edu) Create an account. Username:Demo Password:phage2009http://gowiki.tamu.edu