GUDMAP

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GUDMAP - Analysis Help

Clicking on the Analysis button from the GUDMAP gene expression home page gives three further options:

Microarray Visualisation

• The Microarray Visualisation tool allows users to cluster the first ~1000 Affy probes from a cDNA microarray data series.
• First, select a series dataset from the pull-down menu. Descriptions of the data series can be found at the following link: http://www.gudmap.org/gudmap/pages/series_browse.html
• If you wish, you can filter the data further by changing filter parameters. Choose a hierarchical clustering method and a distance measure and click on 'Cluster' to generate a heatmap of the data series.
• The heatmap is a graphical method of visualising gene expression data. Drag the cursor over a section of heatmap to zoom in on that area. Details of the Affy probe and corresponding gene symbol appear adjacent to each row in the zoom viewer. Clicking on a gene symbol opens up details of this gene at the MGI. More details of the samples in a data series can be found from the following link: http://www.gudmap.org/gudmap/pages/series_browse.html

Microarray Tissue Analysis

• Pairwise comparisons of cDNA microarray data can be found from this page by clicking on ‘Summary’ adjacent to each tissue.
• Pairwise comparison data can be downloaded in .xls format.
• In some instances, more details of pairwise comparisons have been provided. For example, for the kidney it is possible to view an array gene list with links to ISH data by clicking on the link adjacent to ‘Summary’ (i.e. ‘Kidney’).
• Other features of this page are currently under development.

Microarray Components Genelist

• By comparing cDNA microarrays from various laser-capture microdissected components, the GUDMAP consortium has generated top-ranked lists of gene expression for 15 anatomical structures in the developing metanephros.
• Click on a Gene List (e.g. 223_all) to view a list as a Heatmap.
• Click on column headers to reorder the Heatmap. Please note that there may be multiple probes (Affy IDs) for a single gene.