Methodology of spatial pattern comparisons and subsequent heirarchical clustering used in EMAGE






Raw Data Image


Spatial Annotation





For example, Jaccard Index similarity values of the patterns denoting combined strongest, moderate and weakest signal intensities for the Pax6, Sox10 and Dlx5 examples above would be:







  Viewing Option 1

An interactive tree viewer can be started straight from the web browser by clicking a button. You can click on the tree and view heat map representations of sites in the embryo that express the genes on each branch. The contributing raw data images for the selected branch may also be viewed. A slider tool is available to select multiple branches from the tree, and the tree can also be searched for examples of a gene of interest or EMAGE IDs:

We recommend you increase the Java memory on your computer to load large trees (>300 branches) using this method.




  Viewing Option 2

The images are simply arranged (left to right) in rows according to the order (top to bottom) that they appear in the relatedness tree described above. This places the images into blocks that display similarities of expression pattern (but provides no information as to the tree structure).





Viewing Option 3

You can load the approriate .cdt, .gtr and.atr files (these can be downloaded from the relevant EMAGE cluster analysis page) into the original version of JavaTreeView that was developed by Michael Eisen for viewing the output of clustered microarray data. It can be downloaded here. Note that no images can be loaded into this version of JavaTreeView so it is of limited use for visual assessment of in situ expression data.




Quicksearch Help

(Click the icon to keep this page displayed.)