Bioinformatics

Functionalities of BioMart

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Every analysis with BioMart starts by selecting a BioMart database that we want to use. The first step is to check which services are available in BioMart web. The function listMarts() is used when we are going to show all available BioMart web services.

BioMart databases can have many datasets, for Ensembl every species is a different dataset. In the next step, we look at which datasets are present in the selected BioMart by using the function listDatasets().

We can update the Mart object to select a dataset by using the function useDataset(). 

The getBM() function has three arguments that are: 

  1. Filters
  2. Attributes
  3. Values

When there is a need for query restriction, we use Filters. For example we want to restrict the output to all genes present on the human X chromosome then the filter chromosome_name can be used with value ‘X’. The listFilters() function shows us all available filters in the selected dataset.

Attributes are used when we are interested in to retrieve the required values. For example we want to retrieve the gene symbols or chromosomal coordinates. The listAttributes() function shows all available attributes in the selected dataset. In case of multiple filters, the values argument requires a list of values where each position in the list corresponds to the position of the filters in the filters argument. “mart”  is an object of class Mart, which is generated by the useMart() function.

The functions listDatasets(), listAttributes(), and listFilters() are used to return every available option for their respective types. However, this can be unwieldy when the list of results is long, involving much scrolling to find the entry we are interested in. 

Many filters have a predefined list of values that are known to be in the dataset they are associated with. A common example would be the names of chromosomes when searching a dataset at Ensembl.

To save time and computing resources, BioMart will try to identify when we are re-running a query we have executed before. Each time a new query is run, the results will be saved to a cache on our computer. If a query is identified as having been run previously, rather than submitting the query to the server, the results will be loaded from the cache.

Finding of genes in BioMart

Use the “Count” button, apply “Filter” to restrict our query and use “Fetch” to search specific information and then check that box.

Finding of full list of Human genes

Select attributes that we want to know, expand genes and click on the result button. We can also select all to show the whole list of genes. We can check the box to retrieve unique results and these results can be downloaded either in compressed form or simple form.  We can also retrieve gene ontologies by using BioMart. 

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