Comparing expression of undifferentiated cells using ENCODE - which data sets?

Question

[BioinfGuru]

Hi all,

I have developed a pipeline for predicting tissue specificity that currently includes expression data from 26 adult mouse tissues. I have been asked to find genes specific to pre-adipocytes. As undifferentiated cells, I am assuming that it would be a good idea to include their precursor - mesenchymal embryonic fibroblasts (MEFs) in the pipeline. I am also considering including available data (ENCODE) from other mesenchymal precursors (megakaryocyte) or even mesenchymal stem cells. However, this means the set of tissues will include adult and embryonic data. Is this a problem?

Does anyone have any advice here?

Thanks KEnneth.