FLAME: View published data  Print-icon

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

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

    Result: GenePattern displays its main page.

  3. Click a sample name in the table below.
  4. 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.

  5. Optionally, modify the channels to plot parameter.
  6. 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).

  7. Click Run.
  8. 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 .


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
112206D_0minLymphocytes 112206E_0minLymphocytes 112206F_0minLymphocytes
112206G_0minLymphocytes 112206H_0minLymphocytes 112206I_0minLymphocytes
112206J_0minLymphocytes 112206K_0minLymphocytes 112206L_0minLymphocytes
121106A_0minLymphocytes 121106B_0minLymphocytes 121106C_0minLymphocytes
121106D_0minLymphocytes 121206A_0minLymphocytes 121206B_0minLymphocytes
121206C_0minLymphocytes 121206D_0minLymphocytes 121206E_0minLymphocytes
Updated on May 20, 2011 20:00