sigclust in Verhaak GBM cancer cell 2010

Question

[oriolebaltimore]

Dear group, Could anyone help, how Verhaak et al. used sigClust in their Cancer Cell paper. Verhaak et al used GBM expression matrix from TCGA (202 samples x 1740 genes). They obtained 4 clusters as meaningful using consensuscluster.

The described cluster significance was evaluated using SigClust (Liu et al 2008) to find class boundaries were statisticall significant. Finally the authors described the significance as a pairwise table

                   Cluster-PN  Cluster-N    Cluster-CL   Cluster-MES

Cluster-N vs. Cluster-PN < 0.001

Cluster-CL vs. Cluster-PN < 0.001

Cluster-MES vs Cluster-PN < 0.001

Cluster-MES vs Cluster-N < 0.001

Cluster-MES vs Cluster-CL < 0.001

Cluster-N vs. Cluster-CL < 0.001

SigClust takes a matrix of data (genes and samples).

How Verhaak et al. obtained this table and significance of pairwise classes? Could anyone help please.

The output from sigClust is complicated and no proper documentation is provided.

Thanks Adrian

Answer 1

[mark.ebbert]

My response is very late, but hopefully will help someone else.

There is now SigClust2 that has better documentation, and produces a nice visual of the results. Great tool.