ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2009
Defining developmental potency and cell lineage trajectories by expression profiling of differentiating mouse embryonic stem cells.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed.
- The transcription factor E2A drives neural differentiation in pluripotent cells.Development (Cambridge, England) · 2020Article
- Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors.Stem cells (Dayton, Ohio) · 2020Article
- Reconstructing the Temporal Progression of Biological Data Using Cluster Spanning Trees.IEEE transactions on nanobioscience · 2017Article
- Comparative computational analysis of pluripotency in human and mouse stem cells.Scientific reports · 2015Article
- Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast.Nature communications · 2014Article
- Chromatin properties of regulatory DNA probed by manipulation of transcription factors.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Unprecedented cell-selection using ultra-quick freezing combined with aquaporin expression.PloS one · 2014Article
- A focused microarray for screening rat embryonic stem cell lines.Stem cells and development · 2013Article
- Identification of transcription factors for lineage-specific ESC differentiation.Stem cell reports · 2013Article
- Zscan4 restores the developmental potency of embryonic stem cells.Nature communications · 2013Article
- Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity.Nature cell biology · 2012Article
- Cnot1, Cnot2, and Cnot3 maintain mouse and human ESC identity and inhibit extraembryonic differentiation.Stem cells (Dayton, Ohio) · 2012Article
- Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers.Bioinformatics (Oxford, England) · 2012Article
- Article
- Learning biomarkers of pluripotent stem cells in mouse.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers.Genome research · 2011Article
- Discovering biological progression underlying microarray samples.PLoS computational biology · 2011Article
- Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity.BMC genomics · 2011Article
- Inference of gene regulation via miRNAs during ES cell differentiation using MiRaGE method.International journal of molecular sciences · 2011Article
- Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states.BMC systems biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Biologists rely on morphology, function and specific markers to define the differentiation status of cells. Transcript profiling has expanded the repertoire of these markers by providing the snapshot of cellular status that reflects the activity of all genes. However, such data have been used only to assess relative similarities and differences of these cells. Here we show that principal component analysis of global gene expression profiles map cells in multidimensional transcript profile space and the positions of differentiating cells progress in a stepwise manner along trajectories starting from undifferentiated embryonic stem (ES) cells located in the apex. We present three 'cell lineage trajectories', which represent the differentiation of ES cells into the first three lineages in mammalian development: primitive endoderm, trophoblast and primitive ectoderm/neural ectoderm. The positions of the cells along these trajectories seem to reflect the developmental potency of cells and can be used as a scale for the potential of cells. Indeed, we show that embryonic germ cells and induced pluripotent cells are mapped near the origin of the trajectories, whereas mouse embryo fibroblast and fibroblast cell lines are mapped near the far end of the trajectories. We suggest that this method can be used as the non-operational semi-quantitative definition of cell differentiation status and developmental potency. Furthermore, the global expression profiles of cell lineages provide a framework for the future study of in vitro and in vivo cell differentiation.
Indexed as
Identifiers
What OpenQuestion holds
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.