Exporting wheat gene data with BioMart, demo

Demo: BioMart

Follow these instructions to guide you through BioMart to answer the following query:

1. What genes are found on chromosome 5D, between 19400000 and 21300000 in wheat?
2. What are the NCBI Gene IDs for these genes?
3. Are there associated functions from the GO (gene ontology) project that might help describe their function?
4. What are their cDNA sequences?  
    
    

Step 1: Choose the database and dataset

Click on BioMart in the top header of any Ensembl Plants page to open BioMart

Step 2: Choose appropriate filters

Step 3.1: Select attributes (features)

Step 4.1: Get the results

Why are there multiple rows for one gene ID? For example, look at the first few rows.

Step 3.2: Select attributes (sequences)

Step 4.2: Get the results

Note: you can use the Go button to export a file.

What did you learn about the wheat genes in this exercise?

Could you learn these things from the Ensembl browser? Would it take longer?  
 
 

For more details on BioMart, have a look at this publication: Kinsella RJ, Kähäri A, Haider S, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database : the Journal of Biological Databases and Curation. 2011 ;2011:bar030. DOI: 10.1093/database/bar030. PMID: 21785142; PMCID: PMC3170168.