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BIOMART          1 of 38
BIOMART• Developed jointly by EBI & CSHL• BioMart is a search engine that can  find multiple terms and put them  into a ta...
BIOMART• A wide variety of analyses and  tasks:SNP (single nucleotide  polymorphism)selection for candidate gene  screen...
General or Specific Data-Tables• All the genes for one species• Or… only genes on one specific  region of a chromosome• Or...
BioMart Data Sets•   Ensembl genes•   Vega genes•   SNPs•   Markers•   Phenotypes•   Gene expression information•   Gene o...
Web Interface                6 of 38
Simple Text-based  Search Engine                    7 of 38
‘Mouse Gene’ Gives Us Results                                8 of 38
A More Complex Query is Not as           Useful                                 9 of 38
BioMart Walkthrough• Glucose-6-phosphate dehydrogenase  (G6PD) human gene located on  chromosome X in cytogenetic band q28...
Information Flow• Choose the species of interest  (Dataset)• Decide what you would like to know  about the genes (Attribut...
Choose „EnsembleGenes 66‟as aprimary database                   12 of 38
Choose „Homosapiens‟ as thespecies ofinterest              13 of 38
On the left narrow the                        gene set by clicking                        “Filters”. In front of          ...
Select  “Chromosome  X”Select “BandStart q28” and“End q28”                 15 of 38
Expand the “GENE”panel.                    16 of 38
Limit to geneswith MIMdisease ID’.Theseassociationshave beendeterminedusing MIM(OnlineMendelianInheritance inMan).        ...
The filters havedetermined our gene set.Click „Count‟ to see howmany genes have passedthese filters.                      ...
The „Count‟  results show 26  human genes out  of 56478 total  genes passed the  filters.Click on „Attributes‟ toselect ou...
Expand the „GENE‟panel.                    20 of 38
Select, along with the default                                   options, „Associated Gene                                ...
Expand the „EXTERNAL’panel to select ExternalReferences.                           22 of 38
Select „EntrezGene ID‟ and„Mim Morbid Accession‟and„MIM MorbidDescription‟.                             23 of 38
Click „RESULTS‟to preview theoutput.                  24 of 38
To save a file of                           the complete                           table, click „Go‟.Go back and changeFil...
Result         26 of 38
Select ‟Sequences‟                             and then expand the                             „SEQUENCES‟ section.To view...
Expand                        the                        „SEQUEN                        CES‟                        panel ...
Choose „EnsemblGene ID‟, „AssociatedGeneName‟, „Chromosome‟,and „EnsemblTranscript ID‟                        29 of 38
Click „Results‟                  30 of 38
31 of 38
Many BioMarts have now beeninstalled by external groups, inlarge part because of itsautomated deployment tools andcompatib...
Central Serverwww.biomart.org                  33 of 38
WormBase           34 of 38
HapMapPopulationfrequenciesInter-populationcomparisonsGeneannotation                       35 of 38
DictyBase            36 of 38
Uniprot, MSD               37 of 38
GRAMENERice, Maize, Arabidopsis genomes…                                    38 of 38
Thanks         39 of 38
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Biomart

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A walk through biomart..!!!

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Transcript of "Biomart"

  1. 1. BIOMART 1 of 38
  2. 2. 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! 2 of 38
  3. 3. BIOMART• A wide variety of analyses and tasks:SNP (single nucleotide polymorphism)selection for candidate gene screeningmicroarray annotationrecovery of disease links, sequence variations and expression patterns 3 of 38
  4. 4. 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 4 of 38
  5. 5. BioMart Data Sets• Ensembl genes• Vega genes• SNPs• Markers• Phenotypes• Gene expression information• Gene ontology• Homology predictions• Protein annotation 5 of 38
  6. 6. Web Interface 6 of 38
  7. 7. Simple Text-based Search Engine 7 of 38
  8. 8. ‘Mouse Gene’ Gives Us Results 8 of 38
  9. 9. A More Complex Query is Not as Useful 9 of 38
  10. 10. 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? 10 of 38
  11. 11. 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 …) 11 of 38
  12. 12. Choose „EnsembleGenes 66‟as aprimary database 12 of 38
  13. 13. Choose „Homosapiens‟ as thespecies ofinterest 13 of 38
  14. 14. 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 14 of 38
  15. 15. Select “Chromosome X”Select “BandStart q28” and“End q28” 15 of 38
  16. 16. Expand the “GENE”panel. 16 of 38
  17. 17. Limit to geneswith MIMdisease ID’.Theseassociationshave beendeterminedusing MIM(OnlineMendelianInheritance inMan). 17 of 38
  18. 18. The filters havedetermined our gene set.Click „Count‟ to see howmany genes have passedthese filters. 18 of 38
  19. 19. The „Count‟ results show 26 human genes out of 56478 total genes passed the filters.Click on „Attributes‟ toselect output options (i.e.what we would like toknow about our geneset). 19 of 38
  20. 20. Expand the „GENE‟panel. 20 of 38
  21. 21. Select, along with the default options, „Associated Gene name‟ (this shows the gene symbol from HGNC).Note the summary of selectedoptions. The order of attributesdetermines the order ofcolumns in the result table. 21 of 38
  22. 22. Expand the „EXTERNAL’panel to select ExternalReferences. 22 of 38
  23. 23. Select „EntrezGene ID‟ and„Mim Morbid Accession‟and„MIM MorbidDescription‟. 23 of 38
  24. 24. Click „RESULTS‟to preview theoutput. 24 of 38
  25. 25. To save a file of the complete table, click „Go‟.Go back and changeFilters or Attributes ifdesired. Or, View ALLrows as HTML… 25 of 38
  26. 26. Result 26 of 38
  27. 27. Select ‟Sequences‟ and then expand the „SEQUENCES‟ section.To view sequences, go backto „Attributes‟ 27 of 38
  28. 28. Expand the „SEQUEN CES‟ panel and select cDNA sequencesExpand the „HeaderInformation‟ section. 28 of 38
  29. 29. Choose „EnsemblGene ID‟, „AssociatedGeneName‟, „Chromosome‟,and „EnsemblTranscript ID‟ 29 of 38
  30. 30. Click „Results‟ 30 of 38
  31. 31. 31 of 38
  32. 32. Many BioMarts have now beeninstalled by external groups, inlarge part because of itsautomated deployment tools andcompatibility cross differentplatforms. Some of the groupsare model organism databasessuch as Gramene, Dictybase,Wormbase, HapMap variation. 32 of 38
  33. 33. Central Serverwww.biomart.org 33 of 38
  34. 34. WormBase 34 of 38
  35. 35. HapMapPopulationfrequenciesInter-populationcomparisonsGeneannotation 35 of 38
  36. 36. DictyBase 36 of 38
  37. 37. Uniprot, MSD 37 of 38
  38. 38. GRAMENERice, Maize, Arabidopsis genomes… 38 of 38
  39. 39. Thanks 39 of 38
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