Methodology article
Comparing independent microarray studies: the case of human embryonic stem cells
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* Corresponding author: Marcelo O Magnasco magnasco@rockefeller.edu
1 Center for Studies in Physics and Biology, The Rockefeller University. 1230 York Ave, Box 212, New York, NY 10021, U.S.A
2 Department Laboratory of Molecular Vertebrate Embryology, Camridge, The Rockefeller University. 1230 York Ave, Box 32, New York, NY 10021, U.S.A
BMC Genomics 2005, 6:99 doi:10.1186/1471-2164-6-99
Published: 22 July 2005Abstract
Background
Microarray studies of the same phenomenon in different labs often appear at variance because the published lists of regulated transcripts have disproportionately small intersections. We demonstrate that comparing studies by intersecting lists in this manner is methodologically flawed by reanalyzing three studies of the molecular signature of "stemness" in human embryonic stem cells. There are only 7 genes common to all three published lists, suggesting disagreement.
Results
Carefully reanalyzing all three together from the raw data we detect 111 genes upregulated and 95 downregulated in all three studies. The upregulated list was subject to rtRTPCR analysis and 75% of the genes were confirmed.
Conclusion
Our findings show that the three studies have a substantial core of common genes, which is missed if only the published lists are examined. Combined analysis of multiple experiments can be a powerful way to distil coherent conclusions.