title: The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data.
abstract: BACKGROUND
  Inference of gene regulatory networks from high throughput measurement of gene and protein expression is particularly attractive because it allows the simultaneous discovery of interactive molecular signals for numerous genes and proteins at a relatively low cost.
  
  
  RESULTS
  We developed two score-based local causal learning algorithms that utilized the Markov blanket search to identify direct regulators of target mRNAs and proteins. These two algorithms were specifically designed for integrated high throughput RNA and protein data. Simulation study showed that these algorithms outperformed other state-of-the-art gene regulatory network learning algorithms. We also generated integrated miRNA, mRNA, and protein expression data based on high throughput analysis of primary trophoblasts, derived from term human placenta and cultured under standard or hypoxic conditions. We applied the new algorithms to these data and identified gene regulatory networks for a set of trophoblastic proteins found to be differentially expressed under the specified culture conditions.
authors.affiliation: Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA.
authors.forename: Tianjiao
authors.initials: T
authors.lastname: Chu
authors.affiliation: Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA.
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Mouillet
authors.affiliation: Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Hood
authors.affiliation: Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Conrads
authors.affiliation: Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA Magee-Womens Research Institute, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, 15213 USA, Women's Health Integrated Research Center at Inova Health System, Annandale, VA, 22003 USA and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213 USA.
authors.forename: Yoel
authors.initials: Y
authors.lastname: Sadovsky
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism; D014327:Trophoblasts / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D011506:Proteins; D012333:RNA, Messenger; D014157:Transcription Factors