Data Mining in Ensembl with BioMart

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Data Mining in Ensembl with BioMart
www.ensembl.org/biomart/martview www.biomart.org/b
iomart/martview
Nov, 2009
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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 mouse 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 an InterPro domain

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The First Step Choose the Dataset
Dataset Current Ensembl, Human genes
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The Second Step Filters
Filters Define a gene set
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Attributes attach information
Attributes Determine output columns
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Results
Tables or sequences
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Query

• For the human CFTR gene, can I export the
  EntrezGene ID, and also, probes with this gene
  sequence from the Affy HG U133 Plus 2
  microarray platform?
• In the query
• Filters what we know
• Attributes what we want to know.

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Query

• For the human CFTR gene, can I export the
  EntrezGene ID, and also, probes with this gene
  sequence from the Affy HG U133 Plus 2
  microarray platform?
• In the query
• Filters what we know
• Attributes what we want to know.

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Query

• For the human CFTR gene, can I export the
  EntrezGene ID, and also, probes with this gene
  sequence from the Affy HG U133 Plus 2
  microarray platform?
• In the query
• Filters what we know
• Attributes what we want to know (columns in
  the result table)

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A Brief Example
Use the current Ensembl (archives are also
available)
Select Homo sapiens
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Select the genes with Filters
Expand the REGION panel.
Click Filters
Expand the GENE panel to enter in the gene ID(s).
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Filters
Change this to HGNC symbol. Enter CFTR in the
box.
Click Count to see if genes passed through your
filters.
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Attributes (Output Options)
Expand the GENE section.
Click on Attributes
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Attributes (Output Options)
Select Description and Associated Gene Name.
Expand the EXTERNAL panel for non-Ensembl IDs.
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Attributes (Output)
.
External IDs include EntrezGene IDs and also
Microarray probe IDs.
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The Results Table - Preview
For the full result table click Go or View
ALL rows.
Results show Description, Name, EntrezGene and
Probe matches from the Affy HG U133-Plus-2
platform.
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Full Result Table
Affy HG probe
Gene Name
EntrezGene ID
Ensembl Gene and Transcript IDs
Description
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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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BioMart Data Sets

• Ensembl genes
• Vega genes
• Variations

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BioMart around the world
BioMart started at EnsemblTo where has it
travelled?
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Central Portal
www.biomart.org
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WormBase
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HapMap
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(No Transcript)
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GRAMENE
www.gramene.org
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The Potato Center
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How to Get There

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

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The Flow

• Choose Dataset (All genes for a species)
• Choose Filters (narrows the gene set)
• Choose Attributes (output options)
• Now Try the Worked Example on Page 23!

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Ensembl Core Databases

• Relational Database
• Normalised
• Each data point stored only once
• Therefore
• Quick updates
• Minimal storage requirements
• But
• Many tables
• Many joins for complicated queries
• Slow for data mining applications

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Normalised Schema
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BioMart Database

• Data warehouse
• De-normalised
• Query-optimised
• Therefore
• Fast and flexible
• Ideal for data mining
• But
• Tables with apparent redundancy
• Needs rebuilding from scratch for every release
  from normalised core databases

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De-Normalised Schema
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Information Flow
DATASET
FILTER
ATTRIBUTES