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Data Mining in Ensembl with BioMart

Data Mining in Ensembl with BioMart. Giulietta Spudich EBI, 2007. BioMart. http://www.biomart.org/biomart/martview http://www.ensembl.org/biomart/martview Or click on ‘BioMart’ from Ensembl. BioMart- Data mining.

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Data Mining in Ensembl with BioMart

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  1. Data Mining in Ensembl with BioMart Giulietta Spudich EBI, 2007

  2. BioMart http://www.biomart.org/biomart/martview http://www.ensembl.org/biomart/martview • Or click on ‘BioMart’ from Ensembl

  3. BioMart- Data mining • BioMart filters the data in the Ensembl databases, combines multiple terms and puts them into a table format. • Such as: human genes (HGNC IDs), chromosome and base pair position • No programming required!

  4. General or Specific Data-Tables • All the genes for one species • Or… only genes on one specific region of a chromosome • Or… only genes on one specific region of a chromosome that have homologues

  5. Web Interface Dataset Filters: Define the gene set Attributes: Output information Three main stages: Dataset, Filters and Attributes.

  6. Results Tables or sequences

  7. Export tables as… • Microsoft Excel (xls) • Text (csv, tsv) • HTML • GFF • XML Or export sequences in FASTA format

  8. FASTA sequences • Gene (unspliced) • Transcript (cDNA) • Translation (coding) • UTR (5’ or 3’) • Flanking sequence

  9. BioMart – Other Installations Find more at www.biomart.org

  10. The Flow • Choose Dataset (All genes for a species) • Choose Filters (narrows the gene set) • Choose Attributes (output options)

  11. Query: • The human gene encoding Glucose-6-phosphate dehydrogenase (G6PD) is located on chromosome X in cytogenetic band q28. What other genes related to human disease locate to the same region? Do they have Interpro domains? Filters: what we know Attributes: what we want to know.

  12. Query: • The human gene encoding Glucose-6-phosphate dehydrogenase (G6PD) is located on chromosome X in cytogenetic band q28. What other genes related to human disease locate to the same region? Do they have Interpro domains? Filters: what we know Attributes: what we want to know.

  13. BioMart team • Arek Kasprzyk • Syed Haider • Richard Holland • Damian Smedley

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