A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas.
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.
Assou
Said
S
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
Le Carrour
Tanguy
T
Tondeur
Sylvie
S
Ström
Susanne
S
Gabelle
Audrey
A
Marty
Sophie
S
Nadal
Laure
L
Pantesco
Véronique
V
Réme
Thierry
T
Hugnot
Jean-Philippe
JP
Gasca
Stéphan
S
Hovatta
Outi
O
Hamamah
Samir
S
Klein
Bernard
B
De Vos
John
J
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
D006133:Growth Substances; D014157:Transcription Factors