Data Mining in Ensembl with BioMart

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Data Mining in Ensembl with BioMart
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Simple Text-based Search Engine
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Mouse Gene Gives Us Results
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A More Complex Query is Not as Useful
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BioMart- Data mining

• 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
• No programming required!

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General or Specific Data-Tables

• All the genes for one species
• Or only genes on one specific region of a
  chromosome
• Or genes on one region of a chromosome
  associated with a disease

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BioMart Data Sets

• Ensembl genes
• Vega genes
• SNPs
• Markers
• Phenotypes
• Gene expression information
• Gene ontology
• Homology predictions
• Protein annotation

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Web Interface
With BioMart, quickly extract gene-associated
information from the Ensembl databases.
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Information Flow

• Choose the species of interest (Dataset)
• Decide what you would like to know about the
  genes (Attributes)
• (sequences, IDs, description)
• Decide on a smaller geneset using Filters.
• (enter IDs, choose a region )

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Web Interface
Choose the species of interest
Choose what information to view.
Choose the gene set using what we know.
Three main stages Dataset, Attributes and
Filters.
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The First Step Choose the Dataset
Homo sapiens genes are the default.
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The Second Step Attributes
Four output pages.
Attributes are what we want to know about the
genes.
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The SNP Attribute Page
Output variation information such as SNP
reference ID and alleles.
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Filters Allow Gene Selection
Choose the gene set by region, gene ID(s),
protein/domain type.
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Export Sequence or Tables
Genes and attributes are exported as sequence
(Fasta format) or tables.
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Query

• For all mouse genes on chromosome 10 that are
  protein coding, I would like to know the IDs in
  both Ensembl and MGI.
• In the query
• Attributes what we want to know.
• Filters what we know

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Query

• For all mouse genes on chromosome 10 that are
  protein coding, I would like to know the IDs in
  both Ensembl and MGI.
• In the query
• Attributes what we want to know.
• Filters what we know

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Query

• For all mouse genes on chromosome 10 that are
  protein coding, I would like to know the IDs in
  both Ensembl and MGI.
• In the query
• Attributes what we want to know.
• Filters what we know

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A Brief Example
Change dataset to mouse Mus musculus
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A Brief Example
Dataset has changed.
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Attributes (Output Options)
Click Attributes.
Click on GENE.
Attributes allow us to choose what we wish to
know. IDs are found in the Features page.
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Attributes (Output Options)
Ensembl Gene ID is selected
Default options selected Ensembl Gene ID and
Transcript ID
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Attributes (Output Options)
Markersymbol ID will give us the MGI ID
Scroll down to select MGI symbol. Also select the
accession number.
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The Results Table
Results give us Gene IDs for all mouse genes in
the Ensembl database.
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Select a Smaller Gene Set
Expand the REGION panel
Select Filters
Instead of all mouse genes, select protein coding
genes on chromosome 10.
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Select Genes on Chromosome 10
Select chromosome 10
Instead of all mouse genes, select protein coding
genes on chromosome 10.
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Select Protein Coding Genes
Gene type protein coding
Filters are set to chromosome 10 and
protein-coding genes. Genes must meet BOTH
criteria to be in the result table.
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Results (Preview)
For the full result table Go
This is a preview- if you are happy with the
table, click Go.
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Full Result Table
Transcript ID
MGI symbol
MGI Accession Number
Ensembl Gene ID
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Original Query

• For all mouse genes on chromosome 10 that are
  protein coding, I would like to know the IDs in
  both Ensembl and MGI.
• In the query
• Attributes columns in the Result Table
• Filters what we know

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Other Export Options (Attributes)

• 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

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Central Server
www.biomart.org
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WormBase
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HapMap
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(No Transcript)
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Uniprot, MSD
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GRAMENE
Rice, Maize, Arabidopsis genomes
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How to Get There

• Either www.biomart.org/biomart/martview
• Or click on BioMart from Ensembl

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Arek Kasprzyk Benoît Ballester Syed
Haider Richard Holland Damian Smedley
Thanks
Q

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