FLAME: View published data

Pyne et al. (2009) present three datasets in their manuscript. Analysis results for the T cell phosphorylation data are available on the GenePattern ftp site. To view the clusters identified by FLAME for a given sample in this published data, use the FLAMEContourViewer.Pipeline. The pipeline first runs the FLAMEContourDataGenerator module to generate the data required to display a 3-D contour plot of the clusters in a given sample. It then opens the FLAMEViewer to display a 3-D scatterplot and 3-D contour plot of the clusters in the sample.

To launch FLAMEViewer from GenePattern, you need to first install Java 3D as outlined in this FAQ.

To run the pipeline for a given sample from the published data:

  1. Login to the public GenePattern server: http://genepattern.broadinstitute.org/gp/.
    • If you do not have a GenePattern account, you can register on the login page.

      Result: GenePattern displays its main page.

  2. Click a sample name in the table below.
    • The table lists each sample in the T cell phosphorylation dataset.

      Result: GenePattern displays the FLAMEContourViewer.Pipeline page. It automatically populates the parameter fields with the result files for the selected sample.

      Pyne et al. (2009) clustered four channels: SLP76,ZAP70,CD4,CD45RA. The FLAMEViewer uses three channels to display a 3-D contour plot of the clusters in the sample. Select the three channels to use (default: SLP76,ZAP70,CD4).

      Result: GenePattern runs the FLAMEContourDataGenerator to generate data for the 3-D contour plot. It then opens the FLAMEViewer to display both a 3-D scatterplot and 3-D contour plot of the clusters in the sample. For instructions on how to use the viewer, see the FLAMEViewer documentation .

    • Optionally, modify the channels to plot parameter.
  3. Click Run.


The following table lists the samples in the T cell phosphorylation dataset analyzed in Pyne et al. (2009). The parameters used for the analysis are available at ftp://ftp.broadinstitute.org/pub/genepattern/example_files/FLAME/phospho.lymphgated.pipeline.parameters.txt. Use the previous procedure to display analysis results for a selected sample.

090806A_5minLymphocytes 101806D_5minLymphocytes 111306A_5minLymphocytes
111306B_5minLymphocytes 111306C_5minLymphocytes 111306D_5minLymphocytes
111306E_5minLymphocytes 111306F_5minLymphocytes 111306G_5minLymphocytes
112206A_5minLymphocytes 112206B_5minLymphocytes 112206C_5minLymphocytes
112206D_5minLymphocytes 112206E_5minLymphocytes 112206F_5minLymphocytes
112206G_5minLymphocytes 112206H_5minLymphocytes 112206I_5minLymphocytes
112206J_5minLymphocytes 112206K_5minLymphocytes 112206L_5minLymphocytes
121106A_5minLymphocytes 121106B_5minLymphocytes 121106C_5minLymphocytes
121106D_5minLymphocytes 121206A_5minLymphocytes 121206B_5minLymphocytes
121206C_5minLymphocytes 121206D_5minLymphocytes 121206E_5minLymphocytes
090806A_0minLymphocytes 101806D_0minLymphocytes 111306A_0minLymphocytes
111306B_0minLymphocytes 111306C_0minLymphocytes 111306D_0minLymphocytes
111306E_0minLymphocytes 111306F_0minLymphocytes 111306G_0minLymphocytes
112206A_0minLymphocytes 112206B_0minLymphocytes 112206C_0minLymphocytes