Genomic Innovations-Orthology Paralogy

Genomic innovation

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 arerelated 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

http://www.ensembl.org

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…)

3) 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 genesProtein codingChromosome 10

Change dataset to mouse

An example:

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:

An example:

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?