Research Topics
Genomes and Genes | Wen ZhangSummaryAffiliation: University of Toronto Country: Canada Publications
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Detail Information
Publications
Monitoring G-protein-coupled receptor signaling with DNA microarrays and real-time polymerase chain reactionTony Yuen
Department of Neurology, Mount Sinai School of Medicine, New York, New York 10029, USA
Methods Enzymol 345:556-69. 2002
The functional landscape of mouse gene expressionWen Zhang
Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
J Biol 3:21. 2004....- Genome-wide analysis of mouse transcripts using exon microarrays and factor graphsBrendan J Frey
Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
Nat Genet 37:991-6. 2005..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes... - Functional coordination of alternative splicing in the mammalian central nervous systemMatthew Fagnani
Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
Genome Biol 8:R108. 2007..However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood... - Alternative splicing of conserved exons is frequently species-specific in human and mouseQun Pan
CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
Trends Genet 21:73-7. 2005..The results thus provide evidence that species-specific AS of conserved exons constitutes an additional potential source of complexity and species-specific differences between mammals... - Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platformQun Pan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Mol Cell 16:929-41. 2004..These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS... - Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitmentEmily Walker
Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
Cell Stem Cell 1:71-86. 2007..By using this integrative approach, we have formulated novel networks describing gene repression of key developmental regulators in undifferentiated ESCs and successfully predicted the outcomes of genetic manipulation of these networks... - Probing microRNAs with microarrays: tissue specificity and functional inferenceTomas Babak
Banting and Best Department of Medical Research, 112 College St, University of Toronto, Toronto, Ontario M5G 1L6, Canada
RNA 10:1813-9. 2004.... - Zfp206 regulates ES cell gene expression and differentiationWen Zhang
Department of Molecular and Medical Genetics, University of Toronto, 4388 Medical Sciences Building, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
Nucleic Acids Res 34:4780-90. 2006..Together, these data indicate that Zfp206 is a regulator of ES cell differentiation that controls a set of genes expressed very early in development, most of which themselves appear to be regulators... - Exploration of essential gene functions via titratable promoter allelesSanie Mnaimneh
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, ON M5G 1L6, Canada
Cell 118:31-44. 2004..We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection... - High-definition macromolecular composition of yeast RNA-processing complexesNevan J Krogan
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
Mol Cell 13:225-39. 2004..This study provides a high-resolution overview of the modular topology of noncoding RNA-processing machinery... - A panoramic view of yeast noncoding RNA processingWen Tao Peng
Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
Cell 113:919-33. 2003..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA... - A combined 1H-NMR spectroscopy- and mass spectrometry-based metabolomic study of the PPAR-alpha null mutant mouse defines profound systemic changes in metabolism linked to the metabolic syndromeHelen J Atherton
Department of Biochemistry, University of Cambridge, Cambridge, UK
Physiol Genomics 27:178-86. 2006..Furthermore, despite PPAR-alpha being weakly expressed in adipose tissue, a profound metabolic perturbation was detected in this tissue... - Statistical resynchronization and Bayesian detection of periodically expressed genesXin Lu
Department of Statistics, Harvard University, Cambridge, MA 02138, USA
Nucleic Acids Res 32:447-55. 2004.... - Subtractive transcriptomics: establishing polarity drives in vitro human endothelial morphogenesisDavid A Glesne
Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
Cancer Res 66:4030-40. 2006.... - Bim and Noxa are candidates to mediate the deleterious effect of the NF-kappa B subunit RelA in cerebral ischemiaIoana Inta
Department of Neurology, University of Heidelberg, 69120 Heidelberg, Germany
J Neurosci 26:12896-903. 2006..Thus, the deleterious function in cerebral ischemia is specific for the NF-kappaB subunit RelA and may be mediated through Bim and Noxa... - Increased expression of integrin beta1 subunit enhances p21WAF1/Cip1 transcription through the Sp1 sites and p300-mediated histone acetylation in human hepatocellular carcinoma cellsZhengyu Fang
Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, PR China
J Cell Biochem 101:654-64. 2007..Therefore, these findings presented the mechanisms by which integrin beta1 induced the elevated p21 expression in hepatic cancer cells... - Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylationPaul M Evans
Department of Biochemistry and Molecular Biology, Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
J Biol Chem 282:33994-4002. 2007..Our results suggest that KLF4 might function as an activator or repressor of transcription depending on whether it interacts with co-activators such as p300 and CREB-binding protein or co-repressors such as HDAC3... - Positive expression of E-cadherin suppresses cell adhesion to fibronectin via reduction of alpha5beta1 integrin in human breast carcinoma cellsHeng Wu
Key Laboratory of Glycoconjugate Research, Ministry of Health, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, People's Republic of China
J Cancer Res Clin Oncol 132:795-803. 2006..Taken together, these results indicated that positive expression of E-cadherin inhibits the cell adhesion to extracellular matrix mediated by alpha5beta1 integrin signaling... - Distinct functions of homeodomain-containing and homeodomain-less isoforms encoded by homothoraxBarbara Noro
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
Genes Dev 20:1636-50. 2006..We further demonstrate that the mouse ortholog of hth, Meis1, also encodes a HDless isoform, suggesting that homeodomain-less variants of this gene family are evolutionarily ancient... - Novel cross talk of Kruppel-like factor 4 and beta-catenin regulates normal intestinal homeostasis and tumor repressionWen Zhang
Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, Galveston, TX 77555 1048, USA
Mol Cell Biol 26:2055-64. 2006..Our findings suggest that the cross talk of KLF4 and beta-catenin plays a critical role in homeostasis of the normal intestine as well as in tumorigenesis of colorectal cancers... - Gene expression profiling in a renal cell carcinoma cell line: dissecting VHL and hypoxia-dependent pathwaysYide Jiang
Genzyme Molecular Oncology, Framingham, MA 01701, USA
Mol Cancer Res 1:453-62. 2003.... - Integrin beta1 subunit overexpressed in the SMMC-7721 cells regulates the promoter activity of p21(CIP1) and enhances its transcriptionYu Long Liang
Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai 200032, PR China
FEBS Lett 558:107-13. 2004.... - Tumor necrosis factor-like weak inducer of apoptosis-induced neurodegenerationIoana Potrovita
Department of Neurology, University of Heidelberg, D 69120 Heidelberg, Germany
J Neurosci 24:8237-44. 2004..In summary, our data show that TWEAK induces neuronal cell death and is involved in neurodegeneration in vivo... - Preparation of cardiovascular disease-related genes microarray and its application in exploring ligustrazine-induced changes in endothelial gene expressionZesong Li
Beijing Institute of Radiation Medicine, 100850 Beijing, China
Pol J Pharmacol 56:427-33. 2004..This also demonstrates the use of oligonucleotide microarray technology as an approach to studying targets of active components of Traditional Chinese Medicine... - Neuronal activation of NF-kappaB contributes to cell death in cerebral ischemiaWen Zhang
Department of Neurology, University of Heidelberg, Heidelberg, Germany
J Cereb Blood Flow Metab 25:30-40. 2005..In summary, the data show that NF-kappaB is activated in neurons and astrocytes during cerebral ischemia and that NF-kappaB activation in neurons contributes to the ischemic damage... - Expression profiling of homocysteine junction enzymes in the NCI60 panel of human cancer cell linesWen Zhang
Department of Biochemistry, University of Nebraska, Lincoln, Nebraska, USA
Cancer Res 65:1554-60. 2005.... - Down-regulation of PTEN expression due to loss of promoter activity in human hepatocellular carcinoma cell linesDong Zhu Ma
Minstry of Health Key Laboratory of Glycocojugate Research, Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 138 Yixueyuan Road, Shanghai 200032, China
World J Gastroenterol 11:4472-7. 2005..To investigate the regulation of phosphatase and tensin homolog deleted on chromosome ten (PTEN) gene expression in human hepatocellular carcinoma (HCC) cell lines... - Clinical evaluation of oligonucleotide microarrays for the detection of HBV mutants associated with lamivudine resistanceLi-Yan Chen
Beijing Institute of Radiation Medicine, Beijing 100850, China
Pharmacogenomics 6:721-30. 2005..CONCLUSION: The oligonucleotide microarray can be conveniently utilized to detect mutant HBV in clinical serum samples... - Supranormal myocardial creatine and phosphocreatine concentrations lead to cardiac hypertrophy and heart failure: insights from creatine transporter-overexpressing transgenic miceJulie Wallis
Department of Cardiovascular Medicine, University of Oxford, Oxford, England
Circulation 112:3131-9. 2005..These findings caution against the uncritical use of creatine as a therapeutic agent in heart disease... - Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferencesMichael F Berger
Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
Cell 133:1266-76. 2008..Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success...