Description of applet:

This applet visualises the families of probesets associated through MT-links with the given starting probesets. It currently works for the HG-U133A microarray probesets involved in MT families, and allows extending the families with Exon1.0ST probesets

A link to the paper describing the process, and MT families will be linked to from here after publication

To view and use the applet, you require at least the Java 1.4 plugin for your machine. If you don't have Java installed, it is available for free by clicking this link

HG-U133A

Using this applet

Probeset

Enter starting probeset from the HG-U133A array, or from the Exon1.0ST array if the "Exon Array Only" checkbox is checked

Experiment

Choose MAS or RMA pre-processed data. Currently there are 12 arrays from an MCF7/MCF10 study in the database.

Array

Choose the scanned array for the expression and detection call display.

Layout

Choose between Fruchtermann-Reingold or Kamada-Kawai graph layouts. These are implemented in the Jung graph drawing library.

Exon Array Only

Checking this will display only probesets found in the Exon1.0ST microarray.

Link to Exon 1.0

Checking this will show links from transcripts to those probesets found on the Exon1.0ST microarray.

Transcripts

Select whether you wish to see transcripts from RefSeq, Ensembl, or both.

GO!

Clicking this button will run the query and produce the family graph. If a graph is not displayed, it is most likely that the given probeset does not form part of a family.