Open AccessA Meta‐Analysis of Human Embryonic Stem Cells Transcriptome Integrated into a Web‐Based Expression Atlas
Author(s) -
Assou Said,
Le Carrour Tanguy,
Tondeur Sylvie,
Ström Susanne,
Gabelle Audrey,
Marty Sophie,
Nadal Laure,
Pantesco Véronique,
Réme Thierry,
Hugnot JeanPhilippe,
Gasca Stéphan,
Hovatta Outi,
Hamamah Samir,
Klein Bernard,
De Vos John
Publication year - 2007
Publication title -
stem cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.159
H-Index - 229
eISSN - 1549-4918
pISSN - 1066-5099
DOI - 10.1634/stemcells.2006-0352
Subject(s) - biology , sox2 , embryonic stem cell , transcriptome , homeobox protein nanog , wnt signaling pathway , microarray analysis techniques , gene , gene expression profiling , microbiology and biotechnology , genetics , gene expression , induced pluripotent stem cell
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.