title: A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas.
abstract: Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a "consensus hESC gene list." Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This "consensus differentiation gene list" included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, http://amazonia.montp.inserm.fr, to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.
authors.affiliation: Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, 80 Avenue Augustin Fliche, 34295 Montpellier Cedex 5, France. devos@montp.inserm.fr
authors.forename: Said
authors.initials: S
authors.lastname: Assou
authors.forename: Tanguy
authors.initials: T
authors.lastname: Le Carrour
authors.forename: Sylvie
authors.initials: S
authors.lastname: Tondeur
authors.forename: Susanne
authors.initials: S
authors.lastname: Ström
authors.forename: Audrey
authors.initials: A
authors.lastname: Gabelle
authors.forename: Sophie
authors.initials: S
authors.lastname: Marty
authors.forename: Laure
authors.initials: L
authors.lastname: Nadal
authors.forename: Véronique
authors.initials: V
authors.lastname: Pantesco
authors.forename: Thierry
authors.initials: T
authors.lastname: Réme
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Hugnot
authors.forename: Stéphan
authors.initials: S
authors.lastname: Gasca
authors.forename: Outi
authors.initials: O
authors.lastname: Hovatta
authors.forename: Samir
authors.initials: S
authors.lastname: Hamamah
authors.forename: Bernard
authors.initials: B
authors.lastname: Klein
authors.forename: John
authors.initials: J
authors.lastname: De Vos
mesh_terms: D002454:Cell Differentiation; D002874:Chromosome Mapping; D053595:Embryonic Stem Cells / Q000166:cytology / Q000502:physiology*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006133:Growth Substances / Q000235:genetics; D006801:Humans; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D006133:Growth Substances; D014157:Transcription Factors