ArticleStem cells and development2011
Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells.
Article in Stem cells and development, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Functional Annotation ofBiomolecules · 2018Article
- Genetically unmatched human iPSC and ESC exhibit equivalent gene expression and neuronal differentiation potential.Scientific reports · 2017Article
- Characterization of transcriptional modules related to fibrosing-NAFLD progression.Scientific reports · 2017Article
- Entropy-based divergent and convergent modular pattern reveals additive and synergistic anticerebral ischemia mechanisms.Experimental biology and medicine (Maywood, N.J.) · 2016Article
- Quantitative Identification of Compound-Dependent On-Modules and Differential Allosteric Modules From Homologous Ischemic Networks.CPT: pharmacometrics & systems pharmacology · 2016Article
- Article
- Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation.BMC systems biology · 2015Article
- Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells.BMC genomics · 2015Article
- Dynamics of social network structure for Alzheimer and Lymphoma scientific communities.Biology direct · 2015Article
- Computational Models for Transplant Biomarker Discovery.Frontiers in immunology · 2015Review
- Induced Pluripotent Stem Cells Derived from Alzheimer's Disease Patients: The Promise, the Hope and the Path Ahead.Journal of clinical medicine · 2014Review
- Discovery of consensus gene signature and intermodular connectivity defining self-renewal of human embryonic stem cells.Stem cells (Dayton, Ohio) · 2014Article
- Genetic background drives transcriptional variation in human induced pluripotent stem cells.PLoS genetics · 2014Article
- A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells.Stem cell reports · 2014Article
- Article
- A web-server of cell type discrimination system.TheScientificWorldJournal · 2014Article
- Stem cell systems informatics for advanced clinical biodiagnostics: tracing molecular signatures from bench to bedside.Croatian medical journal · 2013Review
- Induced pluripotent stem cells as tools for disease modelling and drug discovery in Alzheimer's disease.Journal of neural transmission (Vienna, Austria : 1996) · 2013Review
- A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.PloS one · 2013Article
- A poor imitation of a natural process: a call to reconsider the iPSC engineering technique.Cell cycle (Georgetown, Tex.) · 2012Review
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Authors and funding
7 authors.
Funding
Abstract
It has been debated whether human induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) express distinctive transcriptomes. By using the method of weighted gene co-expression network analysis, we showed here that iPSCs exhibit altered functional modules compared with ESCs. Notably, iPSCs and ESCs differentially express 17 modules that primarily function in transcription, metabolism, development, and immune response. These module activations (up- and downregulation) are highly conserved in a variety of iPSCs, and genes in each module are coherently co-expressed. Furthermore, the activation levels of these modular genes can be used as quantitative variables to discriminate iPSCs and ESCs with high accuracy (96%). Thus, differential activations of these functional modules are the conserved features distinguishing iPSCs from ESCs. Strikingly, the overall activation level of these modules is inversely correlated with the DNA methylation level, suggesting that DNA methylation may be one mechanism regulating the module differences. Overall, we conclude that human iPSCs and ESCs exhibit distinct gene expression networks, which are likely associated with different epigenetic reprogramming events during the derivation of iPSCs and ESCs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.