BioMart: Find genes associated with array probes
Here are two affymetrix probeset IDs from my microarray experiment that seem to map uniquely to genes in the chicken genome:
(a) Retrieve for the genes corresponding to these probe-sets the Ensembl Gene and Transcript IDs as well as their gene symbols and descriptions.
(b) In order to analyse these genes for possible promoter/enhancer elements, retrieve the 2000 bp upstream of the transcripts of these genes.
(c) In order to be able to study these chicken genes in duck, identify their duck orthologues. Also retrieve the genomic coordinates of these orthologues.
(a) Click New. Choose the Ensembl Genes database. Choose the Chicken genes dataset.
Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input microarray probes/probesets ID list - AFFY Chicken probe ID(s) and enter the list of probeset IDs in the text box (either comma separated or as a list).
Count shows three genes match this list of probesets.
Click on Attributes in the left panel. Select the Features attributes page. Expand the GENE section by clicking on the + box. In addition to the default selected attributes, select Gene name and Gene description. Expand the EXTERNAL section by clicking on the + box. Select AFFY Chicken probe from the Microarray probes/probesets section.
Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file. Tick the box Unique results only.
Your results should show that the 2 probes map to 2 Ensembl genes.
(b) Don’t change Dataset and Filters – simply click on Attributes.
Select the Sequences category. Expand the SEQUENCES tab by clicking on the + box. Select Flank (Transcript) and enter 2000 in the Upstream flank text box. Expand the HEADER INFORMATION tab by clicking on the + box. Select Gene description and Gene name in addition to the default selected attributes.
Note: Flank (Transcript) will give the flanks for all transcripts of a gene with multiple transcripts. Flank (Gene) will give the flanks for one possible transcript in a gene (the most 5’ coordinates for upstream flanking).
Click the Results button on the toolbar.
(c) You can leave the Dataset and Filters the same, and go directly to the Attributes section:
Click on Attributes in the left panel. Select the Homologues category. Expand the GENE tab by clicking on the + box. Select Gene name. Unselect Transcript stable ID and Transcript stable ID version. Expand the ORTHOLOGUES [A-E] tab by clicking on the + box. Select Duck gene stable ID, Duck chromosomes/scaffold name, Duck chromosome/scaffold start (bp) and Duck chromosome/scaffold end (bp).
Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.
Your results should show that for each chicken gene, one duck orthologue has been identified.