Data Mining with BioMart

1
Data Mining with BioMart
2
Simple and Complex Queries

• Genes within a candidate region
• Gene products with a particular protein domain
• Genomic location and description of all mouse and
  rat homologues of all human genes, that have
  transmembrane domains, are known to be expressed
  in the cardiovascular system and are associated
  with non-synonymous SNPs

3
BioMart
BioMart (http//www.biomart.org) is a
query-oriented data management system Developed
jointly by the European Bioinformatics Institute
(EBI) and Cold Spring Harbor Laboratory
(CSHL) Powered by BioMart software

• DroSpeGe
• ArrayExpress DW
• GermOnLine
• PRIDE
• PepSeeker
• Pancreatic Expression Database
• Reactome

• Central Server
• Ensembl
• HapMap
• Dictybase
• Wormbase
• Gramene
• Rat Genome Database

4
BioMart
5
BioMart
Step 1 (Dataset) Choose your database
species Step 2 (Filters) Limit your
dataset Step 3 (Attributes) Specify what
information you want to output Step 4
(Results) Preview and output the results
6
BioMart
Example Retrieve the Enseml Gene, Transcript
and Peptide ID and description of all Ensembl
genes located on band q23 on chromosome 10 of
rat.
7
BioMart - Step 1 (Dataset)
Start a new BioMart query
8
BioMart - Step 1 (Dataset)
Select the Ensembl Gene database
9
BioMart - Step 1 (Dataset)
Databases ENSEMBL ( Ensembl genes) Genomic
Features ( BAC clones / markers) SNP Vega (
Vega genes) Compara homology Compara multiple
alignments Compara pairwise alignments WORMBASE
(CSHL) RGD GENES (MCW)
10
BioMart - Step 1 (Dataset)
Select rat
11
BioMart - Step 2 (Filters)
Filter for genes on cytogenetic band q23 on chr 10
12
BioMart - Step 3 (Attributes)
Output Ensembl Gene, Transcript and Peptide ID
and Description
13
BioMart - Step 4 (Results)
Preview part of the results
14
BioMart - Step 4 (Results)
Export all results in MS Excel format
15
What About Queries Not Possible to Do in BioMart?

• MySQL queries on ensembldb.ensembl.org
• MySQL client
• Perl API
• BioPerl and Ensembl modules

16
Q

A
Q U E S T I O N S A N S W E R S
17
Exercises
The range and complexity of the questions you
can address through the Ensembl MartView resource
is truly impressive. We really encourage you to
spend some time playing with it