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BIOMART

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BIOMART

• Developed jointly by EBI & CSHL• 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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BIOMART

• A wide variety of analyses and tasks:

SNP (single nucleotide polymorphism)

selection for candidate gene screening

microarray annotationrecovery of disease links, sequence

variations and expression patterns

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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

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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 Walkthrough

• Glucose-6-phosphate dehydrogenase (G6PD) human gene located on chromosome X in cytogenetic band q28.

• Which are the other genes in relevance to human diseases locate to the same band?

• Find out their Ensembl Gene IDs and Entrez Gene IDs?

• And also find out their cDNA sequences?

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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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Choose ‘Ensemble Genes 66’as a primary database

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Choose ‘Homo sapiens’ as the species of interest

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On the left narrow the gene set by clicking “Filters”. In front of “REGION”, click on the “+” to expand the choices.

Filters: what we know

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Select “Chromosome X”

Select “Band Start q28” and “End q28”

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Expand the “GENE” panel.

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Limit to genes with MIM disease ID’. These associations have been determined using MIM (Online Mendelian Inheritance in Man).

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The filters have determined our gene set. Click ‘Count’ to see how many genes have passed these filters.

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The ‘Count’ results show 26 human genes out of 56478 total genes passed the filters.

Click on ‘Attributes’ to select output options (i.e. what we would like to know about our gene set).

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Expand the ‘GENE’panel.

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Select, along with the default options, ‘Associated Gene name’ (this shows the gene symbol from HGNC).

Note the summary of selected options. The order of attributes determines the order of columns in the result table.

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Expand the ‘EXTERNAL’ panel to select External References.

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Select ‘EntrezGene ID’ and ‘Mim Morbid Accession’ and‘MIM Morbid Description’.

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Click ‘RESULTS’ to preview the output.

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To save a file of the complete table, click ‘Go’.

Go back and change Filters or Attributes if desired. Or, View ALL rows as HTML…

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Result

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Select ’Sequences’ and then expand the ‘SEQUENCES’ section.

To view sequences, go back to ‘Attributes’

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Expand the ‘SEQUENCES’ panel and select cDNA sequences

Expand the ‘Header Information’ section.

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Choose ‘Ensembl Gene ID’, ‘Associated Gene Name’, ‘Chromosome’, and ‘Ensembl Transcript ID’

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Click ‘Results’

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Many BioMarts have now been installed by external groups, in large part because of its automated deployment tools and compatibility cross different platforms. Some of the groups are model organism databases such as Gramene, Dictybase, Wormbase, HapMap variation.

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Central Server

www.biomart.org

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WormBase

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HapMap

Population frequencies

Inter- population comparisons

Gene annotation

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DictyBase

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Uniprot, MSD

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GRAMENE

Rice, Maize, Arabidopsis genomes…

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Q&AThanks