Find genes associated with array probes
Toyoma et al performed a microarray analysis of zebrafish pineal gland gene expression (Dev Dyn. 2009 Jul; 238(7): 1813–1826). The microarray used was the AFFY Zebrafish probe Array. The top 25 up-regulated probe-sets in the pineal gland of adult zebrafish were:
Dr.10292.1.S1_at Dr.12592.1.S1_at Dr.12469.1.S1_at Dr.12451.1.S1_at Dr.9908.1.A1_at Dr.9853.1.A1_at Dr.9841.1.A1_at Dr.9871.1.A1_at Dr.11305.1.A1_at Dr.8099.1.S1_at Dr.9899.1.S1_at Dr.5738.1.S1_at Dr.9899.1.S2_at Dr.9876.1.S1_at Dr.9835.1.S1_at Dr.8071.1.S1_at Dr.12762.1.A1_at Dr.12451.2.A1_at Dr.352.1.S1_at Dr.14052.1.A1_at Dr.8142.1.S1_at Dr.24898.1.S1_at Dr.15426.1.S1_at Dr.19931.1.S1_at Dr.11085.1.A1_at
(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 human genes in mouse, identify their mouse orthologues. Also retrieve the genomic coordinates of these orthologues.
(a) Click New. Choose the ENSEMBL Genes database. Choose the Danio rerio 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 Zebrafish probeset ID(s) [e.g. Dr.1730.1.A1_at] and enter the list of probeset IDs in the text box (either comma separated or as a list).
Count shows 25 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 Description. Expand the External section by clicking on the + box. Select Affy Zebrafish probeset from the Microarray Attributes 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 25 probes map to 25 Ensembl genes.
(b) Don’t change Dataset and Filters – simply click on Attributes.
Select the Sequences attributes page. Expand the SEQUENCES section by clicking on the + box. Select Flank (Transcript) and enter 2000 in the Upstream flank text box. Expand the Header information section by clicking on the + box. Select, in addition to the default selected attributes, Description and gene name.
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 attributes page. Expand the GENE section by clicking on the + box. Select Gene name. Deselect Ensembl Transcript ID. Expand the ORTHOLOGUES [K-O] section by clicking on the + box. Select Mouse Ensembl Gene ID, Mouse Chromosome Name, Mouse Chr Start (bp) and Mouse Chr End (bp).
Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.