title: Differences in the Early Development of Human and Mouse Embryonic Stem Cells.
abstract: We performed a systematic analysis of gene expression features in early (10-21 days) development of human vs mouse embryonic cells (hESCs vs mESCs). Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms. The similarity is especially evident, when gene expression profiles are clustered together and properties of clustered groups of genes are compared. First 10 days of mESC development match the features of hESC development within 21 days, in accordance with the differences in population doubling time in human and mouse ESCs. At the same time, several important differences are seen. There is a clear difference in initial expression change of transcription factors and stimulus responsive genes, which may be caused by the difference in experimental procedures. However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development. Some groups of genes show peaks of the expression levels during the development and these peaks cannot be claimed to happen at the same time points in the two organisms, as well as for the same groups of (orthologous) genes. We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs. The differences were quantified by comparing promoters of related genes. Most of gene groups behave similarly and have similar transcription factor (TF) binding sites on their promoters. A few groups of genes have similar promoters, but are expressed differently in two species. Interestingly, there are groups of genes expressed similarly, although they have different promoters, which can be shown by comparing their TF binding sites. Namely, a large group of similarly expressed cell cycle-related genes is found to have discrepant TF binding properties in mouse vs human.
authors.affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
authors.forename: R
authors.initials: R
authors.lastname: Gabdoulline
authors.affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
authors.forename: W
authors.initials: W
authors.lastname: Kaisers
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Gaspar
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: K
authors.initials: K
authors.lastname: Meganathan
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: M X
authors.initials: MX
authors.lastname: Doss
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: S
authors.initials: S
authors.lastname: Jagtap
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Hescheler
authors.affiliation: Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 39, 50931 Cologne, Germany.
authors.forename: A
authors.initials: A
authors.lastname: Sachinidis
authors.affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany; Mathematical Institute, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
authors.forename: H
authors.initials: H
authors.lastname: Schwender
mesh_terms: D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D000066449:Human Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D051379:Mice; D000066450:Mouse Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D013045:Species Specificity; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors