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Differences in the Early Development of Human and Mouse Embryonic Stem Cells.

Gabdoulline R, Kaisers W, Gaspar A, Meganathan K, Doss MX, Jagtap S, Hescheler J, Sachinidis A, Schwender H - PLoS ONE (2015)

Bottom Line: Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms.However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development.We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.

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.

No MeSH data available.


Related in: MedlinePlus

Correlation of profiles of gene groups/clusters and individual gene pairs, sorted and drawn as a function of percentage of total number of group/gene pairs.The bold line shows a correlation of expression profiles of the same gene in human vs in mouse. Correlation of average profiles of gene groups are also shown: line with filled circles -clustered using mESC gene expression profiles, line with open circles—clustered using hESC profiles, line with filled squares—co-clustered. The correlations were sorted and drawn as a function of percentage of all group/gene pairs, allowing comparison of cases with different number of pairs. Significance of correlation p<0.05 is at correlation coefficient larger than 0.67 for 9-point expression profiles and 0.71 for 8-point profiles.
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pone.0140803.g004: Correlation of profiles of gene groups/clusters and individual gene pairs, sorted and drawn as a function of percentage of total number of group/gene pairs.The bold line shows a correlation of expression profiles of the same gene in human vs in mouse. Correlation of average profiles of gene groups are also shown: line with filled circles -clustered using mESC gene expression profiles, line with open circles—clustered using hESC profiles, line with filled squares—co-clustered. The correlations were sorted and drawn as a function of percentage of all group/gene pairs, allowing comparison of cases with different number of pairs. Significance of correlation p<0.05 is at correlation coefficient larger than 0.67 for 9-point expression profiles and 0.71 for 8-point profiles.

Mentions: Visual inspection shows that there are high correlations in expression profiles of clustered genes. When quantified by calculating Pearson correlation coefficients, positive correlations can be found for about 90 percent of clusters, see Fig 4. In the same figure, we show the correlation of profiles of individual gene pairs, revealing that about 70% of gene expression profiles are positively correlated. We also performed additional clustering using all expression data points (both for human and mouse) and compared average profiles of separated out human-gene-related time points vs mouse-gene-related time points. The results from this analysis are referred to as “co-clustering” and show similar features as individual gene pairs.


Differences in the Early Development of Human and Mouse Embryonic Stem Cells.

Gabdoulline R, Kaisers W, Gaspar A, Meganathan K, Doss MX, Jagtap S, Hescheler J, Sachinidis A, Schwender H - PLoS ONE (2015)

Correlation of profiles of gene groups/clusters and individual gene pairs, sorted and drawn as a function of percentage of total number of group/gene pairs.The bold line shows a correlation of expression profiles of the same gene in human vs in mouse. Correlation of average profiles of gene groups are also shown: line with filled circles -clustered using mESC gene expression profiles, line with open circles—clustered using hESC profiles, line with filled squares—co-clustered. The correlations were sorted and drawn as a function of percentage of all group/gene pairs, allowing comparison of cases with different number of pairs. Significance of correlation p<0.05 is at correlation coefficient larger than 0.67 for 9-point expression profiles and 0.71 for 8-point profiles.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608779&req=5

pone.0140803.g004: Correlation of profiles of gene groups/clusters and individual gene pairs, sorted and drawn as a function of percentage of total number of group/gene pairs.The bold line shows a correlation of expression profiles of the same gene in human vs in mouse. Correlation of average profiles of gene groups are also shown: line with filled circles -clustered using mESC gene expression profiles, line with open circles—clustered using hESC profiles, line with filled squares—co-clustered. The correlations were sorted and drawn as a function of percentage of all group/gene pairs, allowing comparison of cases with different number of pairs. Significance of correlation p<0.05 is at correlation coefficient larger than 0.67 for 9-point expression profiles and 0.71 for 8-point profiles.
Mentions: Visual inspection shows that there are high correlations in expression profiles of clustered genes. When quantified by calculating Pearson correlation coefficients, positive correlations can be found for about 90 percent of clusters, see Fig 4. In the same figure, we show the correlation of profiles of individual gene pairs, revealing that about 70% of gene expression profiles are positively correlated. We also performed additional clustering using all expression data points (both for human and mouse) and compared average profiles of separated out human-gene-related time points vs mouse-gene-related time points. The results from this analysis are referred to as “co-clustering” and show similar features as individual gene pairs.

Bottom Line: Many development features were found to be conserved, and a majority of differentially regulated genes have similar expression change in both organisms.However, we also found that some biological processes develop differently; this can clearly be shown, for example, for neuron and sensory organ development.We also detected a larger number of upregulated genes during development of mESCs as compared to hESCs.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Biostatistics, Biological Medical Research Center, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.

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.

No MeSH data available.


Related in: MedlinePlus