1. CACAO - Remote training Gene Function and Gene Ontology Fall 2011 http://gowiki.tamu.edu/wiki/index.php/Category:CACAO

2. “Scientists find gene that...”

3. An avalanche of genes High throughput sequencing is finding genes faster than we can understand them Goals for annotation: – Where the genes are in the genome – What their functions are

4. Function annotation Allows us to – Infer the functions of genes Related by common descent Related by similar expression patterns Related by phylogenetic profiles...

5. Function annotation Allows us to – Understand the capabilities of organisms genomes – Understand patterns of gene expression In different environments In different tissues In disease states –...

6. Classic MODel Literature Datasets Curators (rate limiting) Database

7. Requirements Accurate functional annotation for as many genes as possible A system of assigning function that allows both humans and computers to compare, contrast, analyze, and predict gene function Curators to make and/or check these assignments – For CACAO, we will teach you what biocurators do.

8. CACAO Community Assessment – How well can Community – you (with our coaching) Annotation with – assign gene functions Ontologies – using GO?

9. CACAO is competitive Teams get points for complete annotations –GO term (right level of specificity) –reference –evidence code –identify where in the paper the evidence comes from Teams can take away points from competitors by challenging annotations –finding a problem –suggesting a better alternative

10. What’s in it for you (besides credit)? – We hope you will learn how we think about gene function gain skills that will help your future career enjoy contributing to a resource used by people all over the world have fun!

11. The gist of CACAO… Finding evidence (in papers) Making annotations Using GO terms

12. GO = Gene Ontology Controlled vocabulary – Everyone uses the same terms – Terms have IDs that computers can understand Relationships between functions

13. Gene Ontology A common system for describing gene function

14. GO 3 aspects (ontologies) for gene products 1. Biological Process 2. Molecular Function 3. Cellular Component Used to make annotations –aka Gene associations –Term + qualifiers + evidence code + reference etc.

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

16. Biological Process a commonly recognized series of events cell division Figure from Nature Reviews Microbiology 6, 28-40 (January 2008)

17. Cellular Component where a gene product acts

18. Key elements of a GO annotation Submitted to GO consortium Viewable on GONUTS **Don’t worry - I will cover this again (several times)!

19. GO Annotation To make an annotation, you need to – Assign GO terms to genes (gene products) At appropriate level of specificity Sometimes with Qualifiers – NOT – Contributes_to – Colocalizes_with – Record the evidence

20. Record the evidence Where it came from: – Reference (database accession) PMID:6987663 Kind of evidence: – Evidence codes IMP: Inferred from Mutant Phenotype IDA: Inferred from Direct Assay …

21. Community Annotation CACAO - the “Community Annotation” part What I am going to tell you about next is: 1. How to choose proteins to annotate 2. Finding GO terms & navigating a GO term page 3. Finding UniProt accessions 4. Making gene pages on GONUTS & the anatomy of a gene page 5. How and where to add an annotation 6. Where to look for your annotations & other teams’ annotations … (& the challenges!) http://gowiki.tamu.edu/wiki/index.php/

22. Deciding what to annotate 1. randomly 2. topics of interest (ie efflux pump proteins, biofilms) 3. papers you have come across while doing other stuff 4. methods you know or want to learn 5. phenotypes and mutants you are interested in 6. by author 7. by pathway or regulon 8. suggested by another (ie high IEA:manual annotation ratio) 9. current paper mentions another gene product 10. review papers (ie Annual Reviews are excellent sources) EXAMPLE #1: let’s say you have a great paper (PMID:1111) that characterizes the tyrosine kinase activity of your favorite protein (human p53)…

23. Part I: Where do you search for GO terms? GONUTS http://gowiki.tamu.edu

31. CHICK - AgBase (Gallus gallus) dictyBase - dictyBase (Dictyostelium discoideum - slime mold) FB - FlyBase (Drosophila melanogaster) HUMAN - Reactome, BHF-UCL MGI - Mouse genome informatics (Mus musculus - house mouse) SGD - Saccharomyces genome database (Saccharomyces cerevisiase - yeast) TAIR - The Arabidopsis Informatics Resource (Arabidopsis thaliana) WB - WormBase (Caenorhabditis elegans) ZFIN - Zebrafish model organism database (Danio rerio)

32. What do you actually need once you have found the correct term? GO:0004713

33. Part II: You now have a paper, a protein & you found a suitable GO term… what next? UniProt accession - http://www.uniprot.org - Search (“ Query ”) & find the correct UniProt accession for your protein - Look something like: P012A9

34. Part III: Where are you going to add your annotations? GONUTS http://gowiki.tamu.edu

35. How do you make a new gene page in GONUTS? Use the UniProt accession to make a page that you will be able to add your own annotation to. GoPageMaker will: 1.Check if the page exists in GONUTS & take you there if it does. 2.Make a page & pull all of the annotations from UniProt into a table that you can edit.

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39. … Where do you add an annotation? Add a row in the table.

41. What you must fill in (for every annotation) GO:0004713 PMID:1111 IDA: Inferred from direct assay Figure 2a

42. What you might also have to fill in Not sure? Check the competition guidelines. Ask a coach (Jim, Debby, Adrienne or usually me)!

43. Where will your annotation now show up? 1.In the “Annotation” table on the gene page you just edited 2.In the table on your user page http://gowiki.tamu.edu/wiki/index.php/User:Oherrera 3.In the table on your team page http://gowiki.tamu.edu/wiki/index.php/Category:Team_That_Will_Beat_You!!! 4.As points on the scoreboard http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_UW_Parkside

44. Questions? At this point, you should be able to: 1. Find GO terms on GONUTS 2. Find UniProt accessions on UniProt 3. Make a gene page on GONUTS 4. Add an annotation

45. Community Assessment CACAO - the “Community Assessment” part

48. http://gowiki.tamu.edu/wiki/index.php/Category:CACAO_UW_Parkside

49. Example starting from a topic– Shiga toxin PMID:2677606 Make page on GONUTS for Q7BQ98. Has PMID:2677606 been annotated?

50. If it has, search PubMed for a different article. http://www.ncbi.nlm.nih.gov/pubmed?term=2677606 GO:0009405 ? What GO term? (hint: search GONUTS)