Gene set-level network analysis using a toxicogenomics database.

[1]  T. Monks,et al.  The contribution of bromobenzene to our current understanding of chemically-induced toxicities. , 1988, Life sciences.

[2]  Hiroaki Kitano,et al.  Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology , 2002, Current Genetics.

[3]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[4]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[5]  R. Ulrich,et al.  Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. , 2004, Environmental health perspectives.

[6]  M. Saad,et al.  Peroxisomal proliferator-activated receptor alpha deficiency diminishes insulin-responsiveness of gluconeogenic/glycolytic/pentose gene expression and substrate cycle flux. , 2004, Endocrinology.

[7]  Michael D. Waters,et al.  Toxicogenomics and systems toxicology: aims and prospects , 2004, Nature Reviews Genetics.

[8]  Hans Lehrach,et al.  A comparison of oligonucleotide and cDNA-based microarray systems. , 2004, Physiological genomics.

[9]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[10]  Korbinian Strimmer,et al.  An empirical Bayes approach to inferring large-scale gene association networks , 2005, Bioinform..

[11]  Rainer Breitling,et al.  Network theory to understand microarray studies of complex diseases. , 2006, Current molecular medicine.

[12]  G. Kass Mitochondrial involvement in drug-induced hepatic injury. , 2006, Chemico-biological interactions.

[13]  Neil D. Lawrence,et al.  A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription , 2006, Bioinform..

[14]  Hongzhe Li,et al.  Gradient directed regularization for sparse Gaussian concentration graphs, with applications to inference of genetic networks. , 2006, Biostatistics.

[15]  M. Severgnini,et al.  Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment. , 2006, Analytical biochemistry.

[16]  Stephen C. Harris,et al.  Rat toxicogenomic study reveals analytical consistency across microarray platforms , 2006, Nature Biotechnology.

[17]  N. Kiyosawa,et al.  Molecular mechanism investigation of cycloheximide-induced hepatocyte apoptosis in rat livers by morphological and microarray analysis. , 2006, Toxicology.

[18]  Darrell R Boverhof,et al.  Toxicogenomics in risk assessment: applications and needs. , 2006, Toxicological sciences : an official journal of the Society of Toxicology.

[19]  Roland Eils,et al.  Group testing for pathway analysis improves comparability of different microarray datasets , 2006, Bioinform..

[20]  Marco Grzegorczyk,et al.  Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks , 2006, Bioinform..

[21]  T. Urushidani,et al.  Effect of the difference in vehicles on gene expression in the rat liver--analysis of the control data in the Toxicogenomics Project Database. , 2006, Life sciences.

[22]  S. Sahu Hepatotoxicity : from genomics to in vitro and in vivo models , 2007 .

[23]  John Quackenbush,et al.  Seeded Bayesian Networks: Constructing genetic networks from microarray data , 2008, BMC Systems Biology.

[24]  Korbinian Strimmer,et al.  From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data , 2007, BMC Systems Biology.

[25]  Atsushi Ono,et al.  Identification of glutathione depletion-responsive genes using phorone-treated rat liver. , 2007, The Journal of toxicological sciences.

[26]  Adriano V. Werhli,et al.  Reverse Engineering Gene Regulatory Networks with Various Machine Learning Methods , 2008 .

[27]  ChengXiang Zhai,et al.  Inference of gene pathways using mixture Bayesian networks , 2009, BMC Systems Biology.

[28]  Jingtai Han Understanding biological functions through molecular networks , 2008, Cell Research.

[29]  Robert Clarke,et al.  Knowledge-guided multi-scale independent component analysis for biomarker identification , 2008, BMC Bioinformatics.

[30]  N. Kiyosawa,et al.  A toxicogenomics approach for early assessment of potential non-genotoxic hepatocarcinogenicity of chemicals in rats. , 2008, Toxicology.

[31]  T. Urushidani Prediction of Hepatotoxicity Based on the Toxicogenomics Database , 2008 .

[32]  N. Kiyosawa,et al.  Scoring multiple toxicological endpoints using a toxicogenomic database. , 2009, Toxicology letters.

[33]  N. Kiyosawa,et al.  Toxicogenomic Biomarkers for Liver Toxicity , 2009, Journal of toxicologic pathology.