A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequencesMartin Trick
John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
BMC Plant Biol 9:50. 2009
..thaliana. A large number of EST sequences, derived from a range of different Brassica species, are available in the public database, but no public microarray resource has so far been developed for these species...
- Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
Edward K Lobenhofer
Cogenics, Division of Clinical Data, Inc, Morrisville, NC 27560, USA
Genome Biol 9:R100. 2008
..The results of the study demonstrate the classification of histopathological differences, likely reflecting differences in mechanisms of cell-specific toxicity, using either liver tissue or blood transcriptomic data...
Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretationEdward K Lobenhofer
Cogenics, Division of Clinical Data, Morrisville, North Carolina 27560, USA
Toxicol Pathol 34:921-8. 2006
....
- Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments
Gary A Boorman
Environmental Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Toxicol Sci 86:185-93. 2005
..The results of this study demonstrate a prominent circadian rhythm in gene expression in the rat that is a critical factor in planning toxicogenomic experiments...
- Transcriptional profiling of the left and median liver lobes of male f344/n rats following exposure to acetaminophen
Richard D Irwin
Environmental Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Toxicol Pathol 33:111-7. 2005
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- Variation in the hepatic gene expression in individual male Fischer rats
Gary A Boorman
Environmental Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Toxicol Pathol 33:102-10. 2005
..The level of hepatic gene expression under carefully controlled study conditions is less than 1.5-fold for most genes. The impact of individual animal variability on microarray data can be minimized through experimental design...
- Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage
Tong Zhou
Department of Pathology and Laboratory Medicine, Center for Environmental Health and Susceptibility, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Cell Cycle 6:972-81. 2007
..Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization...
- Developmental exposure to diethylstilbestrol alters uterine gene expression that may be associated with uterine neoplasia later in life
Retha R Newbold
Developmental Endocrinology and Endocrine Disruptor Section, Laboratory of Molecular Toxicology, NIEHS, Research Triangle Park, North Carolina 27709, USA
Mol Carcinog 46:783-96. 2007
..These data suggested altered gene expression profiles observed 2 wk after treatment ceased, were established at the time of developmental exposure and maybe related to the initiation events resulting in carcinogenesis...
- Hepatic transcript levels for genes coding for enzymes associated with xenobiotic metabolism are altered with age
Kazuhiko Mori
National Institute of Environmental Health Sciences, Research Triangle Park, NC 27701, USA
Toxicol Pathol 35:242-51. 2007
..Alterations that are considered crucial to the interpretation of long-term study results could then be confirmed by subsequent metabolic studies...
- Multicenter study of acetaminophen hepatotoxicity reveals the importance of biological endpoints in genomic analyses
Richard P Beyer
University of Washington, and Fred Hutchinson Cancer Research Center, Seattle, Washington 98195, USA
Toxicol Sci 99:326-37. 2007
..We show that phenotypic anchoring of gene expression data is required for biologically meaningful analysis of toxicogenomic experiments...
- Receptor-selective coactivators as tools to define the biology of specific receptor-coactivator pairs
Stephanie Gaillard
Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
Mol Cell 24:797-803. 2006
..In this study, we describe the customization of PGC-1alpha and its use to study the biology of the estrogen-related receptor alpha (ERRalpha) in cultured liver cells...
- Rat toxicogenomic study reveals analytical consistency across microarray platforms
Lei Guo
National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
Nat Biotechnol 24:1162-9. 2006
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- The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
Leming Shi
National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
Nat Biotechnol 24:1151-61. 2006
..This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings...
- Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
Tucker A Patterson
National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, USA
Nat Biotechnol 24:1140-50. 2006
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- Profiles of global gene expression in ionizing-radiation-damaged human diploid fibroblasts reveal synchronization behind the G1 checkpoint in a G0-like state of quiescence
Tong Zhou
Department of Pathology and Laboratory Medicine, Center for Environmental Health and Susceptibility, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Environ Health Perspect 114:553-9. 2006
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- Temporal correlation of pathology and DNA damage with gene expression in a choline-deficient model of rat liver injury
Christine L Powell
Curriculum in Toxicology, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7431, USA
Hepatology 42:1137-47. 2005
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- Standardizing global gene expression analysis between laboratories and across platforms
Theodore Bammler
Nat Methods 2:351-6. 2005
..These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used...
- MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues
Omer Barad
Rosetta Genomics, Rehovot, 76706, Israel
Genome Res 14:2486-94. 2004
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- Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference
Shyamal D Peddada
Biostatistics Branch, Laboratory of Molecular Carcinogenesis, Research Triangle Park, NC 27709, USA
Bioinformatics 19:834-41. 2003
..In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal...
- Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells
Leslie C Hodges
Department of Carcinogenesis, UT M.D. Anderson Cancer Center, Smithville, TX 78957, USA
Mol Cancer Res 1:300-11. 2003
..However, cyclin D1 was a key estrogen-induced gene not expressed in response to tamoxifen or raloxifene but constitutively expressed in tamoxifen-resistant cells...
- Regulation of DNA replication fork genes by 17beta-estradiol
Edward K Lobenhofer
Gene Regulation Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Mol Endocrinol 16:1215-29. 2002
..The coexpression of DNA replication fork genes by estrogen without the support of serum growth factors indicates an important estrogen regulatory component of the molecular mechanism driving estrogen-induced mitogenesis...
