Genomic Innovations- Orthology Paralogy

Genomic innovation

Moore, Current opinion in Plant Biology, 2005

Genomic innovation- Paralogy Cotton, Methods in Enzymology, 2005

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

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

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

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

BioMart

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?

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

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

What we want to know about the gene BioMart

Choose a gene set by region, gene ID… BioMart

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

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

Change dataset to mouse An example:

Click on Attributes to choose what we want to know

An example: Click on gene and select gene ID

An example: Click on Filters Expend region

An example: Choose chromosome 10

An example: Expend Gene

An example: Select Gene type: Protein coding

An example: Click on Results

An example:

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?