Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity.

PubWeight™: 1.41‹?› | Rank: Top 5%

🔗 View Article (PMC 4559398)

Published in PLoS One on September 03, 2015

Authors

Hyosil Kim1, Ju-Hwa Kim2, So Youn Kim3, Deokyeon Jo3, Ho Jun Park3, Jihyun Kim3, Sungwon Jung4, Hyun Seok Kim5, KiYoung Lee3

Author Affiliations

1: Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea; Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea.
2: Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea.
3: Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea.
4: Department of Genome Medicine and Science, School of Medicine, Gachon University, Incheon, Korea.
5: Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.

Articles cited by this

Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res (2003) 103.76

Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88

DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79

Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2000) 34.79

The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67

BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res (2003) 18.75

NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res (2012) 15.84

An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42

How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov (2010) 14.09

Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet (2010) 11.82

The IntAct molecular interaction database in 2012. Nucleic Acids Res (2011) 7.49

Online predicted human interaction database. Bioinformatics (2005) 6.83

The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09

Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling. Cell Signal (2012) 5.65

MINT, the molecular interaction database: 2012 update. Nucleic Acids Res (2011) 5.25

ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res (2012) 4.91

CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res (2009) 4.71

The MIPS mammalian protein-protein interaction database. Bioinformatics (2004) 4.66

Concordance of the toxicity of pharmaceuticals in humans and in animals. Regul Toxicol Pharmacol (2000) 4.58

Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res (2012) 2.66

Filter versus wrapper gene selection approaches in DNA microarray domains. Artif Intell Med (2004) 2.46

Toxicity testing in the 21st century: bringing the vision to life. Toxicol Sci (2008) 2.06

Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLS-DA) approach. Hum Genet (2003) 2.01

Development of a large-scale chemogenomics database to improve drug candidate selection and to understand mechanisms of chemical toxicity and action. J Biotechnol (2005) 1.86

CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res (2007) 1.80

MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res (2010) 1.79

mentha: a resource for browsing integrated protein-interaction networks. Nat Methods (2013) 1.60

Regulation of proteasome activity in health and disease. Biochim Biophys Acta (2013) 1.52

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinformatics (2011) 1.50

Oxidative stress-mediated regulation of proteasome complexes. Mol Cell Proteomics (2011) 1.50

Open TG-GATEs: a large-scale toxicogenomics database. Nucleic Acids Res (2014) 1.36

Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the U.S. EPA's ToxRefDB. Reprod Toxicol (2009) 1.22

Validation of putative genomic biomarkers of nephrotoxicity in rats. Toxicology (2008) 1.20

International harmonization of toxicologic pathology nomenclature: an overview and review of basic principles. Toxicol Pathol (2012) 1.17

Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. BMC Genomics (2008) 1.14

A decade of toxicogenomic research and its contribution to toxicological science. Toxicol Sci (2012) 1.14

Investigating the role of P311 in the hypertrophic scar. PLoS One (2010) 1.10

The liver pharmacological and xenobiotic gene response repertoire. Mol Syst Biol (2008) 1.04

A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicol Pathol (2005) 1.03

Data mining reveals a network of early-response genes as a consensus signature of drug-induced in vitro and in vivo toxicity. Pharmacogenomics J (2013) 1.02

Statistical methods for the analysis of high-throughput metabolomics data. Comput Struct Biotechnol J (2013) 1.00

Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database. Toxicology (2009) 0.97

Relationship between hepatic gene expression profiles and hepatotoxicity in five typical hepatotoxicant-administered rats. Toxicol Sci (2005) 0.96

Association study of CSF2RB with schizophrenia in Irish family and case - control samples. Mol Psychiatry (2007) 0.95

Cellular homeostasis and repair in the mammalian liver. Annu Rev Physiol (2015) 0.94

Cathepsin D inhibits oxidative stress-induced cell death via activation of autophagy in cancer cells. Cancer Lett (2012) 0.94

Complement activation in acetaminophen-induced liver injury in mice. J Pharmacol Exp Ther (2012) 0.91

Incorporating Nonlinear Relationships in Microarray Missing Value Imputation. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.91

P311-induced myofibroblasts exhibit ameboid-like migration through RalA activation. Exp Cell Res (2006) 0.89

Effect of chemical mutagens and carcinogens on gene expression profiles in human TK6 cells. PLoS One (2012) 0.88

Potentials and limitations of nonclinical safety assessment for predicting clinical adverse drug reactions: correlation analysis of 142 approved drugs in Japan. J Toxicol Sci (2013) 0.86

NMR study of ligand release from asialoglycoprotein receptor under solution conditions in early endosomes. FEBS J (2012) 0.85

Proteome-wide discovery of mislocated proteins in cancer. Genome Res (2013) 0.83

[Effects of P 311 on the migration of epidermal stem cells in mice with superficial partial-thickness burn and injured cell model in vitro]. Zhonghua Shao Shang Za Zhi (2012) 0.80

Identification of potential genomic biomarkers for early detection of chemically induced cardiotoxicity in rats. Toxicology (2010) 0.78

Critical pathways in heart function: bis(2-chloroethoxy)methane-induced heart gene transcript change in F344 rats. Toxicol Pathol (2006) 0.78