The Connectivity Map (also known as cmap) is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes.
Is it only for cancer?(In this project there are six cancer tissue cell line )
How can we use it for another diseases?
No, connectivity Mapping could be use for other type of disease (in the original science paper, they tried on Obesity and Alzheimer disease, for instance). Your reference dataset will obviously need to be consistent with the type of disease your want to connect to your signature of interest.
We use cmap extensively for just about everything, all you need is a gene signature and an array like dataset to run it on. There's an R implementation in the gCMAP package.
But all the 5 cell lines that they used for microarray are cancer.
The panel of cell lines used by cmap includes MCF7, ssMCF7, HL60, PC3 and SKMEL5.
That just happens to be the dataset they used, it's not hardwired into the software. You can load any array data you like.
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