title: Inferring differentiation pathways from gene expression.
abstract: BACKGROUND
  The regulation of proliferation and differentiation of embryonic and adult stem cells into mature cells is central to developmental biology. Gene expression measured in distinguishable developmental stages helps to elucidate underlying molecular processes. In previous work we showed that functional gene modules, which act distinctly in the course of development, can be represented by a mixture of trees. In general, the similarities in the gene expression programs of cell populations reflect the similarities in the differentiation path.
  
  
  RESULTS
  We propose a novel model for gene expression profiles and an unsupervised learning method to estimate developmental similarity and infer differentiation pathways. We assess the performance of our model on simulated data and compare it with favorable results to related methods. We also infer differentiation pathways and predict functional modules in gene expression data of lymphoid development.
  
  
  CONCLUSIONS
  We demonstrate for the first time how, in principal, the incorporation of structural knowledge about the dependence structure helps to reveal differentiation pathways and potentially relevant functional gene modules from microarray datasets. Our method applies in any area of developmental biology where it is possible to obtain cells of distinguishable differentiation stages.
  
  
  BACKGROUND
  The implementation of our method (GPL license), data and additional results are available at http://algorithmics.molgen.mpg.de/Supplements/InfDif/.
  
  
  BACKGROUND
  Supplementary data is available at Bioinformatics online.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. filho@molgen.mpg.de
authors.forename: Ivan G
authors.initials: IG
authors.lastname: Costa
authors.forename: Stefan
authors.initials: S
authors.lastname: Roepcke
authors.forename: Christoph
authors.initials: C
authors.lastname: Hafemeister
authors.forename: Alexander
authors.initials: A
authors.lastname: Schliep
mesh_terms: D000465:Algorithms; D018797:Cell Cycle Proteins / Q000502:physiology*; D002454:Cell Differentiation / Q000502:physiology*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D018797:Cell Cycle Proteins