Data Mining in Ensembl with BioMart

Data Mining in Ensembl with BioMart www.ensembl.org/biomart/martview www.biomart.org/biomart/martview Nov, 2009

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!

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

The First Step: Choose the Dataset Dataset: Current Ensembl, Human genes

The Second Step: Filters Filters: Define a gene set

Attributes attach information Attributes: Determine output columns

Results Tables or sequences

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.

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)

A Brief Example Use the current Ensembl (archives are also available) Select Homo sapiens

Select the genes with Filters Expand the ‘REGION’ panel. Click Filters Expand the GENE panel to enter in the gene ID(s).

Filters Change this to HGNC symbol. Enter “CFTR” in the box. Click “Count” to see if genes passed through your filters.

Attributes (Output Options) Expand the “GENE” section. Click on ‘Attributes’

Attributes (Output Options) Select “Description” and “Associated Gene Name”. Expand the ‘EXTERNAL’ panel for non-Ensembl IDs.

Attributes (Output) …………………………………………………………………. External IDs include EntrezGene IDs and also Microarray probe IDs.

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.

Full Result Table Affy HG probe Gene Name EntrezGene ID Ensembl Gene and Transcript IDs Description

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

BioMart Data Sets • Ensembl genes • Vega genes • Variations

BioMart around the world… BioMart started at Ensembl…To where has it travelled?

Central Portal www.biomart.org

WormBase

Population frequencies Inter- population comparisons Gene annotation HapMap

DictyBase

GRAMENE www.gramene.org

The Potato Center

How to Get There http://www.biomart.org/biomart/martview http://www.ensembl.org/biomart/martview • Or click on ‘BioMart’ from Ensembl

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!

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

Normalised Schema

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

De-Normalised Schema

Information Flow REGION REGION GENE GENE EXPRESSION EXPRESSION HOMOLOGY HOMOLOGY PROTEIN PROTEIN SNP SNP SPECIES FOCUS SWISSPROT FASTA EMBL GTF REFSEQ HTML GO TEXT INTERPRO EXCEL AFFYMETRIX FILE DATASET FILTER ATTRIBUTES

Data Mining in Ensembl with BioMart