Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for...

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Vydáno v:PeerJ (San Francisco, CA) Ročník 2; s. e618
Hlavní autoři: Mournetas, Virginie, Nunes, Quentin M., Murray, Patricia A., Sanderson, Christopher M., Fernig, David G.
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States PeerJ. Ltd 23.10.2014
PeerJ, Inc
PeerJ Inc
Témata:
Analysis
Biology
Blastocysts
Cell Biology
Cell culture
Cell cycle
Computational Biology
Datasets
Developmental Biology
Embryo cells
Embryonic stem cells
Embryos
Extracellular matrix
Fibroblasts
Gene expression
Genes
Growth factors
Human embryonic stem cells
In silico analysis
Interactome
Meta-analysis
Molecular Biology
Pluripotency
Protein-protein interactions
Proteins
Protein–protein interaction network
Regenerative medicine
Stem cells
Transcription factors
Transcriptome
Human embryonic stem cells
Interactome
Protein–protein interaction network
In silico analysis
Transcriptome
ISSN:2167-8359, 2167-8359
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Abstract Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
AbstractList Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and Results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.
Audience Academic
Author Fernig, David G.
Sanderson, Christopher M.
Nunes, Quentin M.
Murray, Patricia A.
Mournetas, Virginie
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  givenname: Quentin M.
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  organization: Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Keywords Human embryonic stem cells
Interactome
Protein–protein interaction network
In silico analysis
Transcriptome
Language English
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Snippet Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be...
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SubjectTerms Analysis
Biology
Blastocysts
Cell Biology
Cell culture
Cell cycle
Computational Biology
Datasets
Developmental Biology
Embryo cells
Embryonic stem cells
Embryos
Extracellular matrix
Fibroblasts
Gene expression
Genes
Growth factors
Human embryonic stem cells
In silico analysis
Interactome
Meta-analysis
Molecular Biology
Pluripotency
Protein-protein interactions
Proteins
Protein–protein interaction network
Regenerative medicine
Stem cells
Transcription factors
Transcriptome
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Title Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells
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