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

2. 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!

3. 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

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

5. The Second Step: Filters Filters: Define a gene set

6. Attributes attach information Attributes: Determine output columns

7. Results Tables or sequences

8. 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.

9. 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.

10. 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)

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

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

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

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

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

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

17. “Results” show Description, Name, EntrezGene and Probe matches from the Affy HG U133-Plus-2 platform. The Results Table - Preview For the full result table: click “Go” or View “ALL” rows.

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

19. 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

20. BioMart Data Sets Ensembl genes Vega genes Variations

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

22. Central Portal www.biomart.org

23. WormBase

24. HapMap Population frequencies Inter- population comparisons Gene annotation

25. DictyBase

26. GRAMENE www.gramene.org

27. The Potato Center

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

29. 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! The Flow

30. 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

31. Normalised Schema gene_idgene.symbol 9970SMAD1 1712SMAD2 8240SMAD3 1967SMAD4 …… gene_idtranscript 9970ENST00000302085 1712ENST00000262160 1712ENST00000356825 8240ENST00000327367 1967ENST00000342988 …… gene_idstable_id 9970ENSG00000170365 1712ENSG00000175387 8240ENSG00000166949 1967ENSG00000141646 ……

32. 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

33. De-Normalised Schema gene_idtranscript_idgene.symbol ENSG00000170365ENST00000302085SMAD1 ENSG00000175387ENST00000262160SMAD2 ENSG00000175387ENST00000356825SMAD2 ENSG00000166949ENST00000327367SMAD3 ENSG00000141646ENST00000342988SMAD4 ………

34. SPECIES FOCUS REGION SNP PROTEIN HOMOLOGY GENE EXPRESSIONREFSEQ INTERPRO GO SWISSPROT EMBL AFFYMETRIX FASTA FILE EXCEL TEXT GTF HTML DATASETFILTERATTRIBUTES Information Flow REGION SNP PROTEIN HOMOLOGY GENE EXPRESSION