title: Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc.
abstract: BACKGROUND
  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.
  
  
  METHODS
  eegc R package is released under the GNU General Public License within the Bioconductor project, freely available at https://bioconductor.org/packages/eegc/.
  
  
  BACKGROUND
  christine.nardini.rsrc@gmail.com or hongkang.k.mei@gsk.com.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China and University of Chinese Academy of Sciences, Beijing, China.|Computational and Modeling Sciences, Platform Technologies and Science China, Shanghai, GSK.
authors.forename: Xiaoyuan
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Computational and Modeling Sciences, Platform Technologies and Science China, Shanghai, GSK.
authors.forename: Guofeng
authors.initials: G
authors.lastname: Meng
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China and University of Chinese Academy of Sciences, Beijing, China.|CNR IAC "Mauro Picone", Via dei Taurini 19, Roma, Italy.|Personal Genomics S.r.l, Strada Le Grazie 15, Verona, Italy.
authors.forename: Christine
authors.initials: C
authors.lastname: Nardini
authors.affiliation: Computational and Modeling Sciences, Platform Technologies and Science China, Shanghai, GSK.
authors.forename: Hongkang
authors.initials: H
authors.lastname: Mei
mesh_terms: D065150:Cellular Reprogramming; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism* / Q000502:physiology; D062346:Molecular Medicine / Q000379:methods*; D012984:Software; D014157:Transcription Factors
chemical_list: D014157:Transcription Factors