title: Network theory inspired analysis of time-resolved expression data reveals key players guiding P. patens stem cell development.
abstract: Transcription factors (TFs) often trigger developmental decisions, yet, their transcripts are often only moderately regulated and thus not easily detected by conventional statistics on expression data. Here we present a method that allows to determine such genes based on trajectory analysis of time-resolved transcriptome data. As a proof of principle, we have analysed apical stem cells of filamentous moss (P. patens) protonemata that develop from leaflets upon their detachment from the plant. By our novel correlation analysis of the post detachment transcriptome kinetics we predict five out of 1,058 TFs to be involved in the signaling leading to the establishment of pluripotency. Among the predicted regulators is the basic helix loop helix TF PpRSL1, which we show to be involved in the establishment of apical stem cells in P. patens. Our methodology is expected to aid analysis of key players of developmental decisions in complex plant and animal systems.
authors: ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany. h.busch@dkfz.de
authors: Hauke
authors: H
authors: Busch
authors: Melanie
authors: M
authors: Boerries
authors: Jie
authors: J
authors: Bao
authors: Sebastian T
authors: ST
authors: Hanke
authors: Manuel
authors: M
authors: Hiss
authors: Theodhor
authors: T
authors: Tiko
authors: Stefan A
authors: SA
authors: Rensing
mesh_terms: D051792:Basic Helix-Loop-Helix Proteins / Q000502:physiology; D019068:Bryopsida / Q000235:genetics* / Q000254:growth & development; D054338:Cell Transdifferentiation / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D063990:Gene Ontology; D018515:Plant Leaves / Q000166:cytology; D013234:Stem Cells / Q000502:physiology*; D013312:Stress, Physiological / Q000235:genetics; D013598:Systems Theory; D046888:Tissue Array Analysis; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome / Q000502:physiology
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D014157:Transcription Factors
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