ArticleBMC genomics2007
Gene function in early mouse embryonic stem cell differentiation.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed, 156 citations in OpenAlex.
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- Gene Expression Underlying Teloblast Formation in Leech (Annelida: Hirudinae).Evolutionary bioinformatics online · 2026Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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- Exploring the Impact of Microgravity on Gene Expression: Dysregulated Pathways and Candidate Repurposed Drugs.International journal of molecular sciences · 2025Article
- The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.Nature communications · 2024Article
- ECDEP: identifying essential proteins based on evolutionary community discovery and subcellular localization.BMC genomics · 2024Article
- A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs.Communications biology · 2023Article
- PALI1 promotes tumor growth through competitive recruitment of PRC2 to G9A-target chromatin for dual epigenetic silencing.Molecular cell · 2022Article
- An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity.Nucleic acids research · 2022Article
- Transcriptome analysis reveals high tumor heterogeneity with respect to re-activation of stemness and proliferation programs.PloS one · 2022Article
- ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation.Genes & development · 2021Article
- Deciphering the Nature ofCancers · 2021Article
- Functional impact of cancer-associated cohesin variants on gene expression and cellular identity.Genetics · 2021Article
- The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events.Genetics, selection, evolution : GSE · 2021Article
- Chaperone-mediated autophagy regulates the pluripotency of embryonic stem cells.Science (New York, N.Y.) · 2020Article
- The functional landscape of the human phosphoproteome.Nature biotechnology · 2020Article
- NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models.Cancers · 2020Article
- Whsc1 links pluripotency exit with mesendoderm specification.Nature cell biology · 2019Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLittle is known about the genes that drive embryonic stem cell differentiation. However, such knowledge is necessary if we are to exploit the therapeutic potential of stem cells. To uncover the genetic determinants of mouse embryonic stem cell (mESC) differentiation, we have generated and analyzed 11-point time-series of DNA microarray data for three biologically equivalent but genetically distinct mESC lines (R1, J1, and V6.5) undergoing undirected differentiation into embryoid bodies (EBs) over a period of two weeks.
resultsWe identified the initial 12 hour period as reflecting the early stages of mESC differentiation and studied probe sets showing consistent changes of gene expression in that period. Gene function analysis indicated significant up-regulation of genes related to regulation of transcription and mRNA splicing, and down-regulation of genes related to intracellular signaling. Phylogenetic analysis indicated that the genes showing the largest expression changes were more likely to have originated in metazoans. The probe sets with the most consistent gene changes in the three cell lines represented 24 down-regulated and 12 up-regulated genes, all with closely related human homologues. Whereas some of these genes are known to be involved in embryonic developmental processes (e.g. Klf4, Otx2, Smn1, Socs3, Tagln, Tdgf1), our analysis points to others (such as transcription factor Phf21a, extracellular matrix related Lama1 and Cyr61, or endoplasmic reticulum related Sc4mol and Scd2) that have not been previously related to mESC function. The majority of identified functions were related to transcriptional regulation, intracellular signaling, and cytoskeleton. Genes involved in other cellular functions important in ESC differentiation such as chromatin remodeling and transmembrane receptors were not observed in this set.
conclusionOur analysis profiles for the first time gene expression at a very early stage of mESC differentiation, and identifies a functional and phylogenetic signature for the genes involved. The data generated constitute a valuable resource for further studies. All DNA microarray data used in this study are available in the StemBase database of stem cell gene expression data 1 and in the NCBI's GEO database.
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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.