Extracting gene list from hierarchical clustering

[cnyh]

We have conducted an experiment where we have sequenced metastases to four different organs. The raw data have been analyzed via TopHat/Bowtie and Cufflinks/Cuffdiff so far. One of the next tasks I've been asked to complete is to perform an unsupervised analysis in the form of hierarchical clustering, and then to use this to select the genes which cluster best with one specific organ. Can anyone advise me as to how I can use Bioconductor to manage this task? Both the hierarchical clustering with all the genes, and the extraction of the gene list itself.

Thanks a lot!

[cnyh]

Might csSpecificity() be what I am looking for, perhaps?