title: Comparing independent microarray studies: the case of human embryonic stem cells.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, Box 212, 1230 York Ave, New York, NY 10021, USA. mayte@babel.rockefeller.edu
authors.forename: Mayte
authors.initials: M
authors.lastname: Suárez-Fariñas
authors.forename: Scott
authors.initials: S
authors.lastname: Noggle
authors.forename: Michael
authors.initials: M
authors.lastname: Heke
authors.forename: Ali
authors.initials: A
authors.lastname: Hemmati-Brivanlou
authors.forename: Marcelo O
authors.initials: MO
authors.lastname: Magnasco
mesh_terms: D002460:Cell Line; D002478:Cells, Cultured; D018076:DNA, Complementary / Q000378:metabolism; D015536:Down-Regulation; D004622:Embryo, Mammalian / Q000166:cytology*; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013234:Stem Cells / Q000166:cytology*; D015854:Up-Regulation
chemical_list: D018076:DNA, Complementary