1. Genomic Innovations- Orthology Paralogy

2. Genomic innovation

3. Moore, Current opinion in Plant Biology, 2005

4. Genomic innovation- Paralogy Cotton, Methods in Enzymology, 2005

5. Homology, Orthology, Paralogy Homology is a relation between a pair of genes that share a common ancestor. Orthology is a relation defined over a pair of homologous genes, where the two genes have emerged through a speciation event Paralogy is a relation defined over a pair of homologous genes that have emerged through a gene duplication A.M. Altenhoff and C. Dessimoz, Inferring Orthology and Paralogy

6. In and out Paralogy In-paralogy if they are paralogs and duplicated after the speciation event of reference Out-paralogy if the duplication event through which they are related to each other predates the speciation event of reference

7. Ensembl A joint project between EMBL - European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) A genome browser for the retrieval of genomic information http://www.ensembl.org

8. BioMart BioMart is a search engine that can find multiple terms and put them into a table format. Such as: human gene (IDs), chromosome and base pair position

9. BioMart

10. 1)Choose the species of interest (Dataset) 2)Decide what you would like to know about the genes (Attributes) (sequences, IDs, description…) 1)Decide on a smaller geneset using Filters. (enter IDs, choose a region …) How does BioMart work?

11. Choose the species of interest Choose the gene set Choose the information you want to view BioMart

12. Choose the species of interest: Homo sapiens is the default BioMart

13. What we want to know about the gene BioMart

14. Choose a gene set by region, gene ID… BioMart

15. What are the gene IDs of all mouse protein coding genes on chromosome 10? An example:

16. What are the gene IDs of all mouse protein coding genes on chromosome 10? An example: Attributes: what we want to know: Gene IDs Filters: What we know: Mouse genes Protein coding Chromosome 10

17. Change dataset to mouse An example:

18. Click on Attributes to choose what we want to know

19. An example: Click on gene and select gene ID

20. An example: Click on Filters Expend region

21. An example: Choose chromosome 10

22. An example: Expend Gene

23. An example: Select Gene type: Protein coding

24. An example: Click on Results

25. An example:

28. Sequences: UTRs, flanking sequences, cDNA and peptides, etc Gene IDs from Ensembl and external sources (MGI, Entrez, etc.) Microarray data Protein Functions/descriptions (Interpro, GO) Orthologous gene sets SNP/ Variation Data What else can we do with BioMart?