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

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

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?

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

Cellular Component from GOC

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

Biological Process transcription from GOC

GO: molecular function GO: molecular function GO: transferase activity GO: transferase activity GO: transferase activity, transferring phosphorus- containing groups GO: transferase activity, transferring phosphorus- containing groups GO: kinase activity GO: kinase activity GO: phosphotransferase activity, alcohol group as acceptor GO: phosphotransferase activity, alcohol group as acceptor GO: catalytic activity GO: catalytic activity GO: carbohydrate kinase activity GO: carbohydrate kinase activity GO: galactokinase activity GO: 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

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 ( Create an account. Username:Demo Password:phage2009http://gowiki.tamu.edu