supervised clustering analysis for gene expression using microarrays

[JulioFinalet]

Hi ,
Does anybody knows the concept of "supervised clustering analysis" in gene expression. I am specially interested in knowing why the word "Supervised" is used in this context.
thanks

[dpryan]

Supevised clustering occurs whenever you incorporate group information or anything else apart from the values being clustered. So, you could perform normal clustering on an expression matrix, or instead perform supervised clustering by incorporating the various treatments (or known outcomes or anything else for that matter) into the clustering algorithm. Here's an example with microarrays where they used cancer as an outcome variable to inform the clustering.

[JulioFinalet]

thanks for your quick reply!!.
so, If I do the clustering using a pre selection of genes based on a prior knowledge about their expression pattern in different previous analysis, can I still call this a "supervised clustering"?

[dpryan]

No, the clustering itself would still be unsupervised. If you gave the clustering algorithm information about how relevant a gene likely is given prior knowledge then that would be supervised clustering.

[JulioFinalet]

this is what I did:
I compared, independently, samples of Cancer A versus samples of Cancer B,C,D ... and samples of non-malignant controls. In total 10 inferences analysis were made. In every one I selected dysregulated genes. Then I selected those genes with the same dysregulation pattern in at least 5 comparions. Interestingly the resulting genes differentiate, in the clustering analysis, almost perfectly Cancer A from anything else in the study. I know this is a kind of trial and error approach, very empirical. So, how can I name this method?. As you say it is not supervised, but is it still unsupervised?