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A walk through biomart..!!!

A walk through biomart..!!!

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    Biomart Biomart Presentation Transcript

    • 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 „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 “REGION”, click on the “+” to expand the choices.Filters: what we know 14 of 38
    • 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). 17 of 38
    • The filters havedetermined our gene set.Click „Count‟ to see howmany genes have passedthese filters. 18 of 38
    • 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
    • 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 selectedoptions. The order of attributesdetermines the order ofcolumns in the result table. 21 of 38
    • 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 changeFilters or Attributes ifdesired. Or, View ALLrows as HTML… 25 of 38
    • Result 26 of 38
    • Select ‟Sequences‟ and then expand the „SEQUENCES‟ section.To view sequences, go backto „Attributes‟ 27 of 38
    • Expand the „SEQUEN CES‟ panel and select cDNA sequencesExpand the „HeaderInformation‟ section. 28 of 38
    • 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 andcompatibility cross differentplatforms. Some of the groupsare model organism databasessuch as Gramene, Dictybase,Wormbase, HapMap variation. 32 of 38
    • 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