1. GO Enrichment analysis COST Functional Modeling Workshop 22-24 April, Helsinki

2. Enrichment Analysis Statistically compare a gene set (e.g., differentially expressed) to a background. genomics, proteomics – all annotations for a species microarrays – all annotations for array gene set Different statistical tests hypergeometric; binomial;, χ2 (chi-square); ; Fisher's exact test RNASeq data analysis effects of tissue-specific gene length biases

3. PMID:21900207 PMID:15994189 PMID:20132535

4. http://www.geneontology.org Determining which classes of gene products are over-represented or under-represented.

5. However….  many of these tools do not support agricultural species  the tools have different computing requirements A list of these tools that can be used for agricultural species is available on the workshop website at the “Summary of Tools for gene expression analysis” link.

6. Evaluating GO tools Some criteria for evaluating GO Tools: 1.Does it include my species of interest (or do I have to “humanize” my list)? 2.What does it require to set up (computer usage/online) 3.What was the source for the GO (primary or secondary) and when was it last updated? 4.Does it report the GO evidence codes (and is IEA included)? 5.Does it report which of my gene products has no GO? 6.Does it report both over/under represented GO groups and how does it evaluate this? 7.Does it allow me to add my own GO annotations? 8.Does it represent my results in a way that facilitates discovery?

7. Some useful expression analysis tools: Database for Annotation, Visualization and Integrated Discovery (DAVID) http://david.abcc.ncifcrf.gov/ AgriGO -- GO Analysis Toolkit and Database for Agricultural Community http://bioinfo.cau.edu.cn/agriGO/ used to be EasyGO chicken, cow, pig, mouse, cereals, dicots includes Plant Ontology (PO) analysis Onto-Express http://vortex.cs.wayne.edu/projects.htm#Onto-Express can provide your own gene association file Funcassociate 2.0: The Gene Set Functionator http://llama.med.harvard.edu/funcassociate/ can provide your own gene association file Ontologizer http://compbio.charite.de/contao/index.php/ontologizer2.html Java based; allows you to upload your own files

9. http://david.abcc.ncifcrf.gov/  functional grouping – including GO, pathways, gene- disease association  ID Conversion  search functionally related genes  regular updates (*)  online support & publications

11. http://bioinfo.cau.edu.cn/agriGO

12. enrichment analysis using either GO or Plant Ontology (PO) > 40 species: chicken, cow, pig, mouse, cereals, poplar, fruits new species added by request GenBank, EMBL, UniProt Affymetrix, Operon, Agilent arrays http://bioinfo.cau.edu.cn/agriGO

13. Onto-Express Onto-Express analysis instructions are Available in onto-express.ppt http://vortex.cs.wayne.edu/projects.htm

14. Species represented in Onto- Express

15. Can upload your own annotations using OE2GO

16. http://llama.med.harvard.edu/funcassociate/

17. http://compbio.charite.de/contao/index.php/ontologizer2.html

18. http://omicslab.genetics.ac.cn/GOEAST

19. microarray analysis "Batch-Genes analysis" allows analysis of HTP data sets: http://omicslab.genetics.ac.cn/GOEAST

21. http://revigo.irb.hr

23. What next? Exercises or working on your own data sets: Working on your own data set continue with adding GO decide what enrichment tool to use for you own data set (what species the tools accept, if the tools allow you to upload you own annotation file, etc) Tutorial 4: GO Enrichment analysis Use tutorial to try different enrichment tools – compare, determine which will work for you data set.