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Biomart

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Urooj Sabar
Urooj Sabar

BioMart is a search engine developed jointly by EBI and CSHL that allows users to find multiple genomic terms and view them in a table format without programming. It provides access to a wide variety of genomic data sets and allows flexible querying and filtering to retrieve specific gene sets and their associated annotations, identifiers, sequences and more for various species. Users can perform tasks like SNP analysis, candidate gene screening, microarray annotation and disease gene discovery through an intuitive web interface.

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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 table format. Such as: human gene (IDs), chromosome and base pair position No programming required! 2 of 38
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
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
BioMart Data Sets Ensembl genes Vega genes SNPs Markers Phenotypes Gene expression information Gene ontology Homology predictions Protein annotation 5 of 38
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. 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
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
Choose Ensemble Genes 66as a primary database 12 of 38
Choose Homo sapiens as the species of interest 13 of 38
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
Select Chromosome X Select Band Start q28 and End q28 15 of 38
Expand the GENE panel. 16 of 38
Limit to genes with MIM disease ID. These associations have been determined using MIM (Online Mendelian Inheritance in Man). 17 of 38
The filters have determined our gene set. Click Count to see how many genes have passed these filters. 18 of 38
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). 19 of 38
Expand the GENE panel. 20 of 38
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. 21 of 38
Expand the EXTERNAL panel to select External References. 22 of 38
Select EntrezGene ID and Mim Morbid Accession andMIM Morbid Description. 23 of 38
Click RESULTS to preview the output. 24 of 38
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 25 of 38
Result 26 of 38
Select Sequences and then expand the SEQUENCES section. To view sequences, go back to Attributes 27 of 38
Expand the SEQUEN CES panel and select cDNA sequences Expand the Header Information section. 28 of 38
Choose Ensembl Gene ID, Associated Gene Name, Chromosome, and Ensembl Transcript ID 29 of 38
Click Results 30 of 38
31 of 38
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. 32 of 38
Central Server www.biomart.org 33 of 38
WormBase 34 of 38
HapMap Population frequencies Inter- population comparisons Gene annotation 35 of 38
DictyBase 36 of 38
Uniprot, MSD 37 of 38
GRAMENE Rice, Maize, Arabidopsis genomes 38 of 38
Thanks 39 of 38

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Biomart

  • 1. BIOMART 1 of 38
  • 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. 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. 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. BioMart Data Sets Ensembl genes Vega genes SNPs Markers Phenotypes Gene expression information Gene ontology Homology predictions Protein annotation 5 of 38
  • 6. Web Interface 6 of 38
  • 7. Simple Text-based Search Engine 7 of 38
  • 8. Mouse Gene Gives Us Results 8 of 38
  • 9. A More Complex Query is Not as Useful 9 of 38
  • 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. 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. Choose Ensemble Genes 66as a primary database 12 of 38
  • 13. Choose Homo sapiens as the species of interest 13 of 38
  • 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. Select Chromosome X Select Band Start q28 and End q28 15 of 38
  • 17. Limit to genes with MIM disease ID. These associations have been determined using MIM (Online Mendelian Inheritance in Man). 17 of 38
  • 18. The filters have determined our gene set. Click Count to see how many genes have passed these filters. 18 of 38
  • 19. 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). 19 of 38
  • 21. 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. 21 of 38
  • 22. Expand the EXTERNAL panel to select External References. 22 of 38
  • 23. Select EntrezGene ID and Mim Morbid Accession andMIM Morbid Description. 23 of 38
  • 24. Click RESULTS to preview the output. 24 of 38
  • 25. 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 25 of 38
  • 26. Result 26 of 38
  • 27. Select Sequences and then expand the SEQUENCES section. To view sequences, go back to Attributes 27 of 38
  • 28. Expand the SEQUEN CES panel and select cDNA sequences Expand the Header Information section. 28 of 38
  • 29. Choose Ensembl Gene ID, Associated Gene Name, Chromosome, and Ensembl Transcript ID 29 of 38
  • 30. Click Results 30 of 38
  • 32. 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. 32 of 38
  • 34. WormBase 34 of 38
  • 36. DictyBase 36 of 38
  • 37. Uniprot, MSD 37 of 38
  • 39. Thanks 39 of 38