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Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc
MOTIVATION: Cells derived by cellular engineering, i.e. differentiation of induced pluripotent stem cells and direct lineage reprogramming, carry a tremendous potential for medical applications and in particular for regenerative therapies. These approaches consist in the definition of lineage-specif...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870561/ https://www.ncbi.nlm.nih.gov/pubmed/28398503 http://dx.doi.org/10.1093/bioinformatics/btx205 |
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author | Zhou, Xiaoyuan Meng, Guofeng Nardini, Christine Mei, Hongkang |
author_facet | Zhou, Xiaoyuan Meng, Guofeng Nardini, Christine Mei, Hongkang |
author_sort | Zhou, Xiaoyuan |
collection | PubMed |
description | MOTIVATION: Cells derived by cellular engineering, i.e. differentiation of induced pluripotent stem cells and direct lineage reprogramming, carry a tremendous potential for medical applications and in particular for regenerative therapies. These approaches consist in the definition of lineage-specific experimental protocols that, by manipulation of a limited number of biological cues—niche mimicking factors, (in)activation of transcription factors, to name a few—enforce the final expression of cell-specific (marker) molecules. To date, given the intricate complexity of biological pathways, these approaches still present imperfect reprogramming fidelity, with uncertain consequences on the functional properties of the resulting cells. RESULTS: We propose a novel tool eegc to evaluate cellular engineering processes, in a systemic rather than marker-based fashion, by integrating transcriptome profiling and functional analysis. Our method clusters genes into categories representing different states of (trans)differentiation and further performs functional and gene regulatory network analyses for each of the categories of the engineered cells, thus offering practical indications on the potential lack of the reprogramming protocol. AVAILABILITY AND IMPLEMENTATION: eegc R package is released under the GNU General Public License within the Bioconductor project, freely available at https://bioconductor.org/packages/eegc/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5870561 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58705612018-04-05 Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc Zhou, Xiaoyuan Meng, Guofeng Nardini, Christine Mei, Hongkang Bioinformatics Original Papers MOTIVATION: Cells derived by cellular engineering, i.e. differentiation of induced pluripotent stem cells and direct lineage reprogramming, carry a tremendous potential for medical applications and in particular for regenerative therapies. These approaches consist in the definition of lineage-specific experimental protocols that, by manipulation of a limited number of biological cues—niche mimicking factors, (in)activation of transcription factors, to name a few—enforce the final expression of cell-specific (marker) molecules. To date, given the intricate complexity of biological pathways, these approaches still present imperfect reprogramming fidelity, with uncertain consequences on the functional properties of the resulting cells. RESULTS: We propose a novel tool eegc to evaluate cellular engineering processes, in a systemic rather than marker-based fashion, by integrating transcriptome profiling and functional analysis. Our method clusters genes into categories representing different states of (trans)differentiation and further performs functional and gene regulatory network analyses for each of the categories of the engineered cells, thus offering practical indications on the potential lack of the reprogramming protocol. AVAILABILITY AND IMPLEMENTATION: eegc R package is released under the GNU General Public License within the Bioconductor project, freely available at https://bioconductor.org/packages/eegc/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-08-15 2017-04-07 /pmc/articles/PMC5870561/ /pubmed/28398503 http://dx.doi.org/10.1093/bioinformatics/btx205 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Original Papers Zhou, Xiaoyuan Meng, Guofeng Nardini, Christine Mei, Hongkang Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title_full | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title_fullStr | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title_full_unstemmed | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title_short | Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc |
title_sort | systemic evaluation of cellular reprogramming processes exploiting a novel r-tool: eegc |
topic | Original Papers |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870561/ https://www.ncbi.nlm.nih.gov/pubmed/28398503 http://dx.doi.org/10.1093/bioinformatics/btx205 |
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