gene expression profiling

Summary

Summary: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

Top Publications

  1. ncbi Analyzing real-time PCR data by the comparative C(T) method
    Thomas D Schmittgen
    Division of Pharmaceutics, College of Pharmacy, Ohio State University, Parks Hall, 500 West 12th Avenue, Columbus, Ohio, OH 43210 USA
    Nat Protoc 3:1101-8. 2008
  2. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa S Cline
    Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nat Protoc 2:2366-82. 2007
  3. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
  4. ncbi TM4 microarray software suite
    Alexander I Saeed
    Department of Bioinformatics, The Institute for Genomic Research, Rockville, MD, USA
    Methods Enzymol 411:134-93. 2006
  5. ncbi Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 126:663-76. 2006
  6. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
  7. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
  8. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
  9. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
  10. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005

Detail Information

Publications300 found, 100 shown here

  1. ncbi Analyzing real-time PCR data by the comparative C(T) method
    Thomas D Schmittgen
    Division of Pharmaceutics, College of Pharmacy, Ohio State University, Parks Hall, 500 West 12th Avenue, Columbus, Ohio, OH 43210 USA
    Nat Protoc 3:1101-8. 2008
    ..This protocol provides an overview of the comparative C(T) method for quantitative gene expression studies. Also presented here are various examples to present quantitative gene expression data using this method...
  2. pmc Integration of biological networks and gene expression data using Cytoscape
    Melissa S Cline
    Institut Pasteur, 25 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
    Nat Protoc 2:2366-82. 2007
    ..These steps provide a broad sample of the types of analyses performed by Cytoscape...
  3. ncbi High-resolution profiling of histone methylations in the human genome
    Artem Barski
    Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
    Cell 129:823-37. 2007
    ..Our data provide new insights into the function of histone methylation and chromatin organization in genome function...
  4. ncbi TM4 microarray software suite
    Alexander I Saeed
    Department of Bioinformatics, The Institute for Genomic Research, Rockville, MD, USA
    Methods Enzymol 411:134-93. 2006
    ..An integrated MIAME-compliant MySQL database is included. This chapter describes each component of the suite and includes a sample analysis walk-through...
  5. ncbi Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
    Kazutoshi Takahashi
    Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606 8507, Japan
    Cell 126:663-76. 2006
    ..These data demonstrate that pluripotent stem cells can be directly generated from fibroblast cultures by the addition of only a few defined factors...
  6. ncbi Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Ali Mortazavi
    Division of Biology, MC 156 29, California Institute of Technology, Pasadena, California 91125, USA
    Nat Methods 5:621-8. 2008
    ..We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices...
  7. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
    ..The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets...
  8. pmc TopHat: discovering splice junctions with RNA-Seq
    Cole Trapnell
    Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA
    Bioinformatics 25:1105-11. 2009
    ..TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites...
  9. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
    ..We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package...
  10. ncbi Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    Ana Conesa
    Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
    Bioinformatics 21:3674-6. 2005
    ..This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process...
  11. pmc Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    Cole Trapnell
    Department of Computer Science, University of Maryland, College Park, Maryland, USA
    Nat Biotechnol 28:511-5. 2010
    ..These results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation...
  12. pmc Full-length transcriptome assembly from RNA-Seq data without a reference genome
    Manfred G Grabherr
    Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:644-52. 2011
    ..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
  13. pmc edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    Mark D Robinson
    Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
    Bioinformatics 26:139-40. 2010
    ..The software may have other applications beyond sequencing data, such as proteome peptide count data...
  14. pmc Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    Ron Edgar
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Lister Hill Center, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 30:207-10. 2002
    ..A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo...
  15. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
    ..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities...
  16. pmc RNA-Seq: a revolutionary tool for transcriptomics
    Zhong Wang
    Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, Connecticut 06520, USA
    Nat Rev Genet 10:57-63. 2009
    ..This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes...
  17. pmc Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    Jo Vandesompele
    Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
    Genome Biol 3:RESEARCH0034. 2002
    ....
  18. ncbi MicroRNA expression profiles classify human cancers
    Jun Lu
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 435:834-8. 2005
    ..These findings highlight the potential of miRNA profiling in cancer diagnosis...
  19. pmc Circulating microRNAs as stable blood-based markers for cancer detection
    Patrick S Mitchell
    Divisions of Human Biology, Clinical Research, and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Proc Natl Acad Sci U S A 105:10513-8. 2008
    ..Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer...
  20. pmc Integrative genomics viewer
    James T Robinson
    Nat Biotechnol 29:24-6. 2011
  21. ncbi Molecular portraits of human breast tumours
    C M Perou
    Department of Genetics, Stanford University School of Medicine, California 94305, USA
    Nature 406:747-52. 2000
    ..The tumours could be classified into subtypes distinguished by pervasive differences in their gene expression patterns...
  22. ncbi Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets
    Claus Lindbjerg Andersen
    Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK 8200 Aarhus N, Denmark
    Cancer Res 64:5245-50. 2004
    ..The presented strategy can be applied to evaluate the suitability of any normalization gene candidate in any kind of experimental design and should allow more reliable normalization of RT-PCR data...
  23. pmc Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    T Sørlie
    Department of Genetics, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
    Proc Natl Acad Sci U S A 98:10869-74. 2001
    ....
  24. ncbi MrBayes 3: Bayesian phylogenetic inference under mixed models
    Fredrik Ronquist
    Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv 18D, SE 752 36 Uppsala, Sweden
    Bioinformatics 19:1572-4. 2003
    ..g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters...
  25. pmc Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
    Roel G W Verhaak
    The Eli and Edythe L Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Cancer Cell 17:98-110. 2010
    ..We provide a framework that unifies transcriptomic and genomic dimensions for GBM molecular stratification with important implications for future studies...
  26. pmc RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
    ..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
  27. pmc RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    Bo Li
    Department of Computer Sciences, University of Wisconsin Madison, Madison, WI, USA
    BMC Bioinformatics 12:323. 2011
    ..A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments...
  28. pmc Significance analysis of microarrays applied to the ionizing radiation response
    V G Tusher
    Departments of Medicine and Biochemistry, Stanford University, 269 Campus Drive, Center for Clinical Sciences Research 1115, Stanford, CA 94305-5151, USA
    Proc Natl Acad Sci U S A 98:5116-21. 2001
    ..Surprisingly, four nucleotide excision repair genes were induced, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation...
  29. pmc A microRNA expression signature of human solid tumors defines cancer gene targets
    Stefano Volinia
    Department of Molecular Virology, Immunology, and Medical Genetics and Cancer Comprehensive Center, Ohio State University, Columbus, OH 43210, USA
    Proc Natl Acad Sci U S A 103:2257-61. 2006
    ..Our results indicate that miRNAs are extensively involved in cancer pathogenesis of solid tumors and support their function as either dominant or recessive cancer genes...
  30. pmc Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
    Marcel H Schulz
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Bioinformatics 28:1086-92. 2012
    ..In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values...
  31. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  32. ncbi Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations
    Michael W Pfaffl
    Physiology, FML Weihenstephan, Centre of Life and Food Science, Technical University of Munich, Germany
    Biotechnol Lett 26:509-15. 2004
    ..The BestKeeper application and necessary information about data processing and handling can be downloaded on http://www.wzw.tum.de/gene-quantification/bestkeeper.html...
  33. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
    ..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
  34. ncbi Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Nat Genet 40:1413-5. 2008
    ..From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels...
  35. ncbi Java Treeview--extensible visualization of microarray data
    Alok J Saldanha
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 20:3246-8. 2004
    ..An applet version is also available that can be used on any website with no special server-side setup...
  36. pmc Integrative genomic profiling of human prostate cancer
    Barry S Taylor
    Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
    Cancer Cell 18:11-22. 2010
    ..The genomic and clinical outcome data from these patients are now made available as a public resource...
  37. pmc NCBI GEO: archive for functional genomics data sets--10 years on
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 39:D1005-10. 2011
    ..This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  38. pmc An integrated genomic analysis of human glioblastoma multiforme
    D Williams Parsons
    Ludwig Center for Cancer Genetics and Therapeutics, and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 321:1807-12. 2008
    ..These studies demonstrate the value of unbiased genomic analyses in the characterization of human brain cancer and identify a potentially useful genetic alteration for the classification and targeted therapy of GBMs...
  39. pmc The transcriptional landscape of the yeast genome defined by RNA sequencing
    Ugrappa Nagalakshmi
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 320:1344-9. 2008
    ..We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated...
  40. pmc A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes
    Richard M Neve
    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, USA
    Cancer Cell 10:515-27. 2006
    ..We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations...
  41. ncbi lumi: a pipeline for processing Illumina microarray
    Pan Du
    Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
    Bioinformatics 24:1547-8. 2008
    ..The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data...
  42. pmc A scaling normalization method for differential expression analysis of RNA-seq data
    Mark D Robinson
    Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
    Genome Biol 11:R25. 2010
    ..We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets...
  43. ncbi MicroRNA gene expression deregulation in human breast cancer
    Marilena V Iorio
    Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
    Cancer Res 65:7065-70. 2005
    ..We could identify miRNAs whose expression was correlated with specific breast cancer biopathologic features, such as estrogen and progesterone receptor expression, tumor stage, vascular invasion, or proliferation index...
  44. pmc qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
    Jan Hellemans
    Center for Medical Genetics, Ghent University Hospital, De Pintelaan, B 9000 Ghent, Belgium
    Genome Biol 8:R19. 2007
    ..These models and algorithms are implemented in qBase, a free program for the management and automated analysis of qPCR data...
  45. ncbi Open source clustering software
    M J L de Hoon
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639 Japan
    Bioinformatics 20:1453-4. 2004
    ..In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C...
  46. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency...
  47. pdf DAVID: Database for Annotation, Visualization, and Integrated Discovery
    Glynn Dennis
    Science Applications International Corporation Frederick, Clinical Services Program, Laboratory of Immunopathogenesis and Bioinformatics, National Cancer Institute at Frederick, MD 21702, USA
    Genome Biol 4:P3. 2003
    ..A more judicious approach is to provide query-based access to an integrated database that disseminates biologically rich information across large datasets and displays graphic summaries of functional information...
  48. ncbi Adjusting batch effects in microarray expression data using empirical Bayes methods
    W Evan Johnson
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA, USA
    Biostatistics 8:118-27. 2007
    ..We illustrate our methods using two example data sets and show that our methods are justifiable, easy to apply, and useful in practice. Software for our method is freely available at: http://biosun1.harvard.edu/complab/batch/...
  49. ncbi DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
    Likun Wang
    MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST Department of Automation, Tsinghua, University, Beijing 100084, China
    Bioinformatics 26:136-8. 2010
    ..In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference...
  50. pmc The developmental transcriptome of Drosophila melanogaster
    Brenton R Graveley
    Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, Connecticut 06030 6403, USA
    Nature 471:473-9. 2011
    ..These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development...
  51. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression...
  52. ncbi Unique microRNA molecular profiles in lung cancer diagnosis and prognosis
    Nozomu Yanaihara
    Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Cancer Cell 9:189-98. 2006
    ..These results indicate that miRNA expression profiles are diagnostic and prognostic markers of lung cancer...
  53. ncbi BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    Steven Maere
    Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
    Bioinformatics 21:3448-9. 2005
    ....
  54. ncbi MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    Oliver Thimm
    Max Planck Institute for Molecular Plant Physiology, Golm, Germany
    Plant J 37:914-39. 2004
    ....
  55. pmc Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
    Sian Jones
    Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
    Science 321:1801-6. 2008
    ..Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis...
  56. pmc Summaries of Affymetrix GeneChip probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 31:e15. 2003
    ..In particular, improvements in the ability to detect differentially expressed genes are demonstrated...
  57. ncbi The primary transcriptome of the major human pathogen Helicobacter pylori
    Cynthia M Sharma
    Max Planck Institute for Infection Biology, RNA Biology Group, D 10117 Berlin, Germany
    Nature 464:250-5. 2010
    ..Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species...
  58. pmc NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses
    Konstantin D Taganov
    Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 103:12481-6. 2006
    ....
  59. ncbi The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    Justin Lamb
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Science 313:1929-35. 2006
    ..These results indicate the feasibility of the approach and suggest the value of a large-scale community Connectivity Map project...
  60. pmc The microRNA.org resource: targets and expression
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
    Nucleic Acids Res 36:D149-53. 2008
    ..The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation...
  61. pmc Alternative isoform regulation in human tissue transcriptomes
    Eric T Wang
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Nature 456:470-6. 2008
    ....
  62. pmc ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
    Helen Parkinson
    Functional Genomics Team, EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 39:D1002-4. 2011
    ..Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy...
  63. pmc The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Genet 41:178-86. 2009
    ....
  64. ncbi Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
    Heidi S Phillips
    Department of Tumor Biology and Angiogenesis, Genentech, Inc, South San Francisco, California 94080, USA
    Cancer Cell 9:157-73. 2006
    ..A robust two-gene prognostic model utilizing PTEN and DLL3 expression suggests that Akt and Notch signaling are hallmarks of poor prognosis versus better prognosis gliomas, respectively...
  65. pmc Understanding mechanisms underlying human gene expression variation with RNA sequencing
    Joseph K Pickrell
    Department of Human Genetics, The University of Chicago, Chicago 60637, USA
    Nature 464:768-72. 2010
    ..Our results illustrate the power of high-throughput sequencing for the joint analysis of variation in transcription, splicing and allele-specific expression across individuals...
  66. pmc GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    Eran Eden
    Molecular Cell Biology Department, Weizmann Institute of Science, Rehovot, Israel
    BMC Bioinformatics 10:48. 2009
    ..A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results...
  67. pmc WGCNA: an R package for weighted correlation network analysis
    Peter Langfelder
    Department of Human Genetics and Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
    BMC Bioinformatics 9:559. 2008
    ..While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial...
  68. pmc An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
    Ittai Ben-Porath
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 40:499-507. 2008
    ....
  69. ncbi A gene-expression signature as a predictor of survival in breast cancer
    Marc J van de Vijver
    Division of Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
    N Engl J Med 347:1999-2009. 2002
    ..A more accurate means of prognostication in breast cancer will improve the selection of patients for adjuvant systemic therapy...
  70. ncbi Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing
    J Cristobal Vera
    Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 17:1636-47. 2008
    ..This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies...
  71. ncbi MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer
    Fanyin Meng
    Department of Internal Medicine, Scott and White Clinic, Texas A and M University System Health Science Center College of Medicine, Temple, Texas, USA
    Gastroenterology 133:647-58. 2007
    ..Although a role for aberrant miRNA expression in cancer has been postulated, the pathophysiologic role and relevance of aberrantly expressed miRNA to tumor biology has not been established...
  72. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter A C 't Hoen
    The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nucleic Acids Res 36:e141. 2008
    ..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies...
  73. ncbi microRNA-directed phasing during trans-acting siRNA biogenesis in plants
    Edwards Allen
    Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
    Cell 121:207-21. 2005
    ....
  74. ncbi TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
    Geo Pertea
    The Institute for Genomic Research, Rockville, MD 20850, USA
    Bioinformatics 19:651-2. 2003
    ..The system can run on multi-CPU architectures including SMP and PVM...
  75. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
    ..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
  76. ncbi Identification of novel transcripts in annotated genomes using RNA-Seq
    Adam Roberts
    Department of Computer Science, UC Berkeley, Berkeley, CA, USA
    Bioinformatics 27:2325-9. 2011
    ..We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation...
  77. pmc Transcriptome genetics using second generation sequencing in a Caucasian population
    Stephen B Montgomery
    Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, 1211 Switzerland
    Nature 464:773-7. 2010
    ..This analysis shows that high throughput sequencing technologies reveal new properties of genetic effects on the transcriptome and allow the exploration of genetic effects in cellular processes...
  78. pmc Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
    H Rosaria Chiang
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:992-1009. 2010
    ....
  79. pmc Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
    Yuichi Taniguchi
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 329:533-8. 2010
    ..At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated...
  80. ncbi Identification of stem cells in small intestine and colon by marker gene Lgr5
    Nick Barker
    Hubrecht Institute, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
    Nature 449:1003-7. 2007
    ..The expression pattern of Lgr5 suggests that it marks stem cells in multiple adult tissues and cancers...
  81. pmc NCBI GEO: archive for high-throughput functional genomic data
    Tanya Barrett
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA
    Nucleic Acids Res 37:D885-90. 2009
    ..This article summarizes the GEO repository structure, content and operating procedures, as well as recently introduced data mining features. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/...
  82. pmc Computation for ChIP-seq and RNA-seq studies
    Shirley Pepke
    Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
    Nat Methods 6:S22-32. 2009
    ....
  83. ncbi A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
    Shiaoching Gong
    GENSAT Project, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 260, New York 10021, USA
    Nature 425:917-25. 2003
    ..The atlas, library of BAC vectors and BAC transgenic mice generated in this screen provide a rich resource that allows a broad array of investigations not previously available to the neuroscience community...
  84. pmc Insights from genomic profiling of transcription factors
    Peggy J Farnham
    Department of Pharmacology and the Genome Center, University of California Davis, Davis, California 95616, USA
    Nat Rev Genet 10:605-16. 2009
    ..It also suggests future experiments that may further our understanding of the causes and consequences of transcription factor-genome interactions...
  85. pmc ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
    Helen Parkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D868-72. 2009
    ..In this update, we describe the ArrayExpress developments over the last two years...
  86. pmc Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
    Akiko Doi
    Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Nat Genet 41:1350-3. 2009
    ....
  87. pmc The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Nat Biotechnol 28:827-38. 2010
    ..The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis...
  88. pmc Most "dark matter" transcripts are associated with known genes
    Harm van Bakel
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
    PLoS Biol 8:e1000371. 2010
    ..We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported...
  89. ncbi A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function
    John D Cahoy
    Department of Neurobiology, Stanford University School of Medicine, Stanford, California 94305, USA
    J Neurosci 28:264-78. 2008
    ....
  90. ncbi Genome-wide insertional mutagenesis of Arabidopsis thaliana
    Jose M Alonso
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
    Science 301:653-7. 2003
    ..Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene...
  91. pmc Comparing de novo assemblers for 454 transcriptome data
    Sujai Kumar
    Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK
    BMC Genomics 11:571. 2010
    ..We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis...
  92. ncbi Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution
    Sohrab P Shah
    Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
    Nature 461:809-13. 2009
    ..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression...
  93. pmc Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
    Thomas L Parchman
    Department of Botany, University of Wyoming, Laramie, WY 82071, USA
    BMC Genomics 11:180. 2010
    ..Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies...
  94. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
    ..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
  95. pmc Human induced pluripotent stem cells free of vector and transgene sequences
    Junying Yu
    Morgridge Institute for Research, Madison, WI 53707 7365, USA
    Science 324:797-801. 2009
    ..These results demonstrate that reprogramming human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors and removes one obstacle to the clinical application of human iPS cells...
  96. pmc Common regulatory variation impacts gene expression in a cell type-dependent manner
    Antigone S Dimas
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, CB10 1HH, Cambridge, UK
    Science 325:1246-50. 2009
    ..As functional variants may be operating in a tissue-dependent manner, we performed gene expression profiling and association with genetic variants (single-nucleotide polymorphisms) on three cell types of 75 ..
  97. pmc An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis
    Matthew P R Berry
    Division of Immunoregulation, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
    Nature 466:973-7. 2010
    ..Our study also provides a broad range of transcriptional biomarkers with potential as diagnostic and prognostic tools to combat the TB epidemic...
  98. pmc RNA-Seq gene expression estimation with read mapping uncertainty
    Bo Li
    Department of Computer Sciences, University of Wisconsin, Madison, WI 53706, USA
    Bioinformatics 26:493-500. 2010
    ..Previous computational methods either discard reads that map to multiple locations or allocate them to genes heuristically...
  99. pmc Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    Tomasz Czechowski
    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Plant Physiol 139:5-17. 2005
    ..The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future...
  100. pmc Identification of novel light-induced genes in the suprachiasmatic nucleus
    Veronica M Porterfield
    School of Biomedical Sciences, Kent State University, Kent, OH 44242 USA
    BMC Neurosci 8:98. 2007
    ..Using laser capture microscopy, microarray analysis, and quantitative real-time PCR, we performed a comprehensive screen for changes in gene expression immediately following a 30 minute light pulse in suprachiasmatic nucleus of mice...
  101. ncbi Transcriptional regulation of cardiac progenitor cell populations
    Amanda M Masino
    Department of Internal Medicine, University of Texas Southwestern Medical Center Dallas, Dallas, TX 75390 8573, USA
    Circ Res 95:389-97. 2004
    ..These results define the transcriptional profile of mammalian cardiac progenitor cells and provide insight into the molecular regulation of the earliest periods of heart development...

Research Grants80

  1. Pilot and definitive studies to evaluate Insertional Mutagenesis
    LU TAYLOR; Fiscal Year: 2012
    ..This study is ongoing and the isolated hepatic RNA will be sent to another contract lab for gene expression profiling. Toxicogenomic evaluation of four rat liver carcinogens and three non-carcinogens in male Fischer 344 ..
  2. Studies to Evaluate the Toxicological Potential of Test Articles
    LU TAYLOR; Fiscal Year: 2010
    ..This study is ongoing and the isolated hepatic RNA will be sent to another contract lab for gene expression profiling. Toxicogenomic evaluation of four rat liver carcinogens and three non-carcinogens in male Fischer 344 ..
  3. Med1 in Liver Metabolism, Regeneration and Cancer
    Janardan K Reddy; Fiscal Year: 2013
    ..b>Gene expression profiling revealed that Med1 upregulates many genes that are important for lipogenesis and gluconeogenesis...
  4. Molecular Markers for Progression of Pulmonary Fibrosis in Systemic Sclerosis
    Shervin Assassi; Fiscal Year: 2013
    ..Under their guidance, the candidate has published the largest gene expression profiling study in systemic sclerosis (SSc) to date. Dr. Jon E...
  5. Metabolic mechanisms of antiestrogen resistance in breast cancer
    UBALDO EMILIO MARTINEZ OUTSCHOORN; Fiscal Year: 2013
    ..We will also perform gene expression profiling (GEP) of the carcinoma cells that I generate to determine if we can generate a signature that predicts ..
  6. Pax8-PPARgamma regulation of transcription and metabolism in thyroid cancer
    RONALD JAY KOENIG; Fiscal Year: 2013
    ..b>Gene expression profiling of PPFP thyroid cancers (compared to all other benign and malignant thyroid neoplasms) resulted in the ..
  7. Pluripotent stem cell-derived HSCs: improvements and molecular mechanisms
    Patrick Cahan; Fiscal Year: 2013
    ..orchestrate and specify the HSC in vivo would guide a more faithful derivation of PSC-HSCs, we performed gene expression profiling of purified HSCs and their immediate precursors at key developmental stages from the mouse embryo (..
  8. Aryl Hydrocarbon Receptor Modulators for the Treatment of Hepatocellular Carcinom
    Siva Kumar Kolluri; Fiscal Year: 2012
    ..3. Shortlist compounds for future in vivo testing by gene expression profiling We will compare the gene expression induced by SAhRMs to distinguish them from the transcriptional ..
  9. Clinical and genomic responses to remote ischemic preconditioning
    Brian W McCrindle; Fiscal Year: 2010
    ..b>Gene expression profiling will be noted at induction of anesthesia before application of the RIPC stimulus, 15 minutes after RIPC ..
  10. SATB1-dependent epigenetic regulation of leukemia initiating cells
    Britta Will; Fiscal Year: 2011
    ..SATB1 binding patterns in AML LIC with low and restored SATB1 expression by ChIP-seq combined with gene expression profiling. Genes differentially occupied and expressed will be further functionally analyzed to determine their ..
  11. Roles of RhoA/Rho-kinase Signaling in Cavernous Neurons Following Axonal Injury
    TRINITY JUDE BIVALACQUA; Fiscal Year: 2013
    ..Improve my understanding of genetics and complement this with studies focused on gene expression profiling and bioinformatics as it relates to disease pathobiology...
  12. Role of estrogen-related receptors in cardiac and skeletal muscle
    Janice M Huss; Fiscal Year: 2010
    ..We will analyze these models with gene expression profiling coupled with chromatin immunoprecipitation to identify target genes for ERRs...
  13. Understanding thyroid hormone regulation of neurogenesis in the cochlea
    Mirna Mustapha; Fiscal Year: 2013
    ..that affect axonal guidance and synaptogenesis in the cochlea using candidates previously identified by gene expression profiling of Pit1dw and normal cochlea and test the functional activity of the proteins encoded by subset of these ..
  14. Serotonin, Autism, and investigating cell types for CNS disorders.
    Joseph D Dougherty; Fiscal Year: 2010
    ..Daniel Geschwind. His dissertation entailed gene expression profiling to identify neural stem and progenitor cell genes, followed by anatomical and functional studies of ..
  15. Inflammation and Repair in Cardiac Ischemia-Reperfusion
    Lewis C Becker; Fiscal Year: 2011
    ..The techniques will include molecular biology, gene expression profiling with cDNA arrays, gene transfer by recombinant adenoviral vectors, transfection of decoy ..
  16. Race-based social stress and health trajectories from adolescence to adulthood
    Jacquelynne S Eccles; Fiscal Year: 2010
    ..cytokine production and immune cell resistance to the anti-inflammatory effects of glucocorticoids, gene expression profiling of leukocytes to identify broad groups of genes associated with social stress (e.g...
  17. Proteome Bead-Display for Discovery of Tumor Antigens
    Mark Lim; Fiscal Year: 2013
    ..of a new TAA for CRC on the Bead-GPSTM platform by using candidate pre-selection with ultra-low noise gene expression profiling;v) demonstration of a MALDI-MSI bead barcoding system capable of generating tens of thousands of unique ..
  18. Cellular Mechanisms for Increased Gluconeogenesis in Type 2 Diabetes
    Varman T Samuel; Fiscal Year: 2013
    ..g. glycerol and glutamine) and unbiased gene expression profiling. The efficacy of PC ASO in lowering endogenous glucose production and improving insulin sensitivity will ..
  19. Genetic correction of human beta-thalassemic induced pluripotent stem cells
    EIRINI PAPAPETROU; Fiscal Year: 2012
    ..of "safe harbor" sites for transgene integration in the human genome, using bioinformatics analyses and gene expression profiling of iPSCs and their differentiated progeny...
  20. The Role of Long Non-coding RNAs in EMT and Cancer Stem Cells
    Jason I Herschkowitz; Fiscal Year: 2013
    ..Research: Gene expression profiling has been used to classify human breast tumors into distinct, clinically- relevant subgroups, including a ..
  21. Transcriptional regulation of enteroendocrine cell differentiation by NeuroD
    Andrew B Leiter; Fiscal Year: 2013
    ..Aim 3 will identify NeuroD regulated genes in normal enteroendocrine cells by gene expression profiling by high throughput sequencing (RNAseq) of RNA from NeuroD+ cells isolated from mouse small intestine by ..
  22. A Systems Biology Approach for Pediatric and Adult Autoimmune Diseases
    MARIA VIRGINIA PASCUAL; Fiscal Year: 2013
    ..Mechanistic studies will utilize gene expression profiling assays to find a novel diagnostic test for JDM as well as disease activity measures and biomarkers to ..
  23. Biomarkers of Sudden Death and Progressive Heart Failure
    GORDON FRANK TOMASELLI; Fiscal Year: 2010
    ..and inflammation, the objectives of this proposal are to develop a transcriptomic biomarker based on gene expression profiling of PBMC in order to identify patients at high risk for SCD and worsening HF...
  24. microRNA analysis of neurons generated from patient-specific iPSCs
    Herbert M Lachman; Fiscal Year: 2013
    ..And, although a number of interesting findings have emerged in studying gene expression profiling in autopsy samples obtained from subjects with schizophrenia (SZ), there are numerous confounding ..
  25. Elucidating the in vivo Role of the p53 Apoptosis-Specific Target Gene Siva
    Jeanine L Frey; Fiscal Year: 2013
    ..Using gene expression profiling, we identified the pro-apoptotic gene Siva (CD27-binding protein), which encodes a protein shown ..
  26. TARGETING G(alpha)q AND SRC-3 SIGNALING AS A NOVEL THERAPEUTIC APPROACH IN MELANO
    Vasiliki Poulaki; Fiscal Year: 2013
    ..Using gene expression profiling analysis after siRNA- mediated silencing of these transcription factors, and chromatin ..
  27. HIF-2alpha mediated mitophagy and lipogenesis in clear cell renal cell carcinoma
    Bo Qiu; Fiscal Year: 2013
    ..Using gene expression profiling, I have identified candidate HIF-2[unreadable] regulated pathways in ccRCC by acutely suppressing HIF-2[..
  28. Histone modifications and respiratory effects of traffic particle exposure
    Lifang Hou; Fiscal Year: 2013
    ..Blood leukocyte gene expression profiling in highly PM-exposed subjects has revealed that systemic inflammatory responses in blood are mediated by ..
  29. Adverse Outcomes of Assisted Reproductive Technologies: Genetics or Epigenetics?
    Margareta Pisarska; Fiscal Year: 2013
    ..In this application, we will use genome-wide genetic, epigenetic, and gene expression profiling to differentiate the impact of infertility genetics and IVF-induced epigenetic changes on placental ..
  30. Genetic correction of human beta-thalassemic induced pluripotent stem cells
    EIRINI PAPAPETROU; Fiscal Year: 2013
    ..of "safe harbor" sites for transgene integration in the human genome, using bioinformatics analyses and gene expression profiling of iPSCs and their differentiated progeny...
  31. Integrated Multidisciplinary Strategies for Detection of Diabetic Retinopathies
    Hao F Zhang; Fiscal Year: 2010
    ..changes of the retina and serum prepared from animals with different duration of diabetes, as well as gene expression profiling of retinal samples, and retinal vascular cells under normal and high glucose, to further identify ..
  32. Chemokine Signals in the Premetastatic Niche Inhibit Metastasis
    Ann Richmond; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Gene expression profiling has indicated that the up-regulation of specific subsets of chemokines/cytokine/ growth factors is often linked to poorer prognosis for women with invasive mammary carcinoma...
  33. Pulmonary Vascular Changes in Early Chronic Obstructive Pulmonary Disease (COPD)
    R Graham Barr; Fiscal Year: 2011
    ..controls) will be characterized with MR and full-lung CT imaging, spirometry, flow cytometry, and gene expression profiling to test the following hypotheses: 1) Functional and structural changes in the pulmonary vasculature and ..
  34. Role of the developmental regulator Gon4-like in B lymphopoiesis
    JOHN D COLGAN; Fiscal Year: 2011
    ..b>Gene expression profiling indicated that decreased Gon4-like expression does not impair activation of B-lineage genes, but does ..
  35. Oncogenic Kit receptor signaling in vivo
    Peter Besmer; Fiscal Year: 2012
    ..Furthermore, gene expression profiling indicates that blocking SFK signaling reduces KitL induced expression of TH2-cytokine genes in BMMC...
  36. High-Content Screening for Peroxisome Biogenesis for Type-II Diabetes.
    JONATHAN ZACHARY SEXTON; Fiscal Year: 2013
    ..b>Gene expression profiling will be performed with compounds stimulating peroxisome biogenesis to identify distinct mechanisms...
  37. Dissecting the Role of HIV-1 Tat &Chemokine Axis in Subtype-Specificity of HAD
    Vinayaka R Prasad; Fiscal Year: 2012
    ..and finally identify cellular genes specifically induced by subtype B Tat protein using differential gene expression profiling. We propose four specific aims...
  38. Investigating gene x environment interaction using human exposures to O3 & LPS
    David B Peden; Fiscal Year: 2010
    ..b>Gene expression profiling using mRNA recovered from airway and circulating cells will also be conducted to identify novel ..
  39. Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
    Charles M Perou; Fiscal Year: 2013
    ..For the second phase of TCGA project, we propose to continue to perform quantitative gene expression profiling of all protein-coding genes, non-protein coding mRNAs(ncRNAs) and microRNAs, on -2000 tumors per year...
  40. Micro-RNA Profiling and Cardiovascular Effects of Traffic Particle Exposure
    Lifang Hou; Fiscal Year: 2012
    ..Blood leukocyte gene expression profiling in highly PM-exposed subjects has revealed that systemic inflammatory responses are initiated through ..
  41. CYTOPROTECTIVE EFFECTS OF INFLAMMATION MEDIATED MEMBRANE REPAIR
    DOUGLAS LOWELL MANN; Fiscal Year: 2013
    ..To further identify the mechanisms for the cytoprotective effects of TRAF2 we performed comparative gene expression profiling in the hearts of MHC-TRAF2 and MHC-TRAF2-DN mice and identified a unique "emergency response gene" ..
  42. The Role of THAP1 in Dystonia
    Mark S Ledoux; Fiscal Year: 2013
    ..Using lymphoblastoid cell lines, transfected cell lines and gene expression profiling, we will determine the effects of individual THAP1 sequence variants on THAP1 expression and function...
  43. Molecular Basis and Consequences of Early Developmental Epigenetic Programming
    David Serre; Fiscal Year: 2013
    ..the genome-wide DNA methylation patterns, using a novel sequencing developed in our lab, and extensive gene expression profiling in multiple tissues...
  44. Targeting renal inflammatory pathways of SLE nephritis in mouse and man
    Anne Davidson; Fiscal Year: 2013
    ..We will use a combination of immuno- histochemistry, flow cytometry, functional studies and gene expression profiling to identify genes that are putative severity/prognostic markers or that are biomarkers for disease onset,..
  45. Deciphering ExPEC Virulence Mechanisms
    Matthew A Mulvey; Fiscal Year: 2012
    ..Here we propose to utilize the zebrafish model system, in association with genetic screens and gene expression profiling, to delineate ExPEC virulence factors and host response pathways that come into play during both ..
  46. TARGETING ONCOGENE EXPRESSION TO SKIN IN TRANSGENIC MICE
    DENNIS ROOP; Fiscal Year: 2013
    ..tumors that developed in these models with a combination of comparative genomic hybridization arrays and gene expression profiling. Our analyses revealed that these models are characterized by a high level of genomic instability and we ..
  47. LONG-TERM OXYGEN TREATMENT TRIAL (LOTT) PHARMACOGENOMICS ANCILLARY STUDY
    Craig P Hersh; Fiscal Year: 2013
    ..peripheral blood for RNA at baseline (pre- randomization) and at follow-up, and perform whole-genome gene expression profiling in 100 LOTT participants randomized to supplemental oxygen to define a set of genes that are ..
  48. Mechanisms of Brd2 immunoprotection from insulin resistance
    Gerald V Denis; Fiscal Year: 2011
    ..Preliminary gene expression profiling studies of human abdominal adipocytes establish that PPAR-gamma levels are negatively correlated with ..
  49. Expression-Based Multi-Gene Signatures for CRC Recurrence and Chemoselection
    Christopher Sears; Fiscal Year: 2012
    ..As a result of the Phase II, AmberGen has developed a promising CRC tumor assay based on multi-gene expression profiling, termed the Praxis-CRCTM...
  50. Molecular pathways leading to chronic graft dysfunction
    VALERIA RAQUEL MAS; Fiscal Year: 2012
    ..We will prospectively study gene expression profiling in graft biopsies at pre-implantation, post reperfusion and during the first 9 months post-KTx...
  51. Role of EZH2 in Epithelial Ovarian Cancer
    Rugang Zhang; Fiscal Year: 2013
    ..whole-genome chromatin immunoprecipitation (ChIP) followed by next generation sequencing analysis and gene expression profiling. Integrative analysis revealed a list of 60 direct EZH2 target genes whose expression was upregulated by ..
  52. STEM CELLS IN PERIPHERAL NERVOUS SYSTEM DEVELOPMENT
    Sean J Morrison; Fiscal Year: 2013
    ..To identify new mechanisms that regulate NCSC function and PNS development, we performed gene expression profiling to identify transcripts that were significantly more highly expressed in fetal gut NCSCs as compared to ..
  53. Genetic Regulation of Complex Neurological Disease
    Wayne N Frankel; Fiscal Year: 2012
    ..b>Gene expression profiling revealed an enrichment of hippocampally-expressed genes that are downregulated in mutants, several of ..
  54. The Rho GTPases Cdc42 and Rac1 in diabetic Nephropathy
    JEFFREY BENTON HODGIN; Fiscal Year: 2013
    ..Constructing a conserved glomerular transcriptional network using genome-wide gene expression profiling from humans and mice, we find Cdc42 to be one of the most important regulatory nodes...
  55. Cytoprotective cytokine signaling and reperfusion injury
    DOUGLAS LOWELL MANN; Fiscal Year: 2010
    ..To further identify the mechanisms for the cytoprotective effects of TRAF2 we performed comparative gene expression profiling in the hearts of MHC-TRAF2 and MHC-TRAF2-DN mice and identified a unique "emergency response gene" ..
  56. Assessing the Notch Pathway as a Therapeutic Target in Lung Cancer Adenocarcinoma
    Khaled Hassan; Fiscal Year: 2013
    ..b>Gene expression profiling of non-small-cell lung cancer specimens has shown elevated expression of downstream effectors of Notch ..
  57. IGF1R: A candidate oncogene in pediatric high grade gliomas
    Claudia P Miller; Fiscal Year: 2012
    ..Additionally, gene expression profiling will allow us to determine the similarities and differences between our mouse model and the human ..
  58. Susceptibility Genes in Primary Sjogren's Sydrome
    KATHY L contact MOSER; Fiscal Year: 2010
    ..Preliminary data generated by our group using gene expression profiling and genome-wide association studies with pooled DNA approaches have identified several key biological ..
  59. Mechanisms of T cell leukemia induction and maintenance
    Iannis Aifantis; Fiscal Year: 2013
    ..In this application we study the mechanism of CNS entry and propose novel targets for future therapy. ..
  60. Neuropeptide Modulation of Taste Signals
    Nirupa Chaudhari; Fiscal Year: 2010
    ..through the following Specific Aims: 1: Which taste cells express oxytocin receptor? Using single cell gene expression profiling and immunocytochemistry, we will test this because cell type has implications for function...
  61. Hormone-Regulated Pathways Controlling Implantation and Fertility
    Milan K Bagchi; Fiscal Year: 2012
    ..DNA microarray-based gene expression profiling and receptor-coregulator analyses have revealed novel steroid-regulated pathways, providing important ..
  62. MicroRNA regulation of human T and B cell activation
    Daniel R Salomon; Fiscal Year: 2013
    ..within this complexity will illuminate the key pathways in a way that cannot be achieved by simple gene expression profiling or proteomics...
  63. Endothelin-2 in Ovarian Follicle Rupture
    Chemyong Ko; Fiscal Year: 2010
    ..Using a gene expression profiling approach, we have identified EDN-2, a potent smooth muscle constrictor, which is exclusively and ..
  64. Program Project,Restoration of Endocrine Pancreas Funct*
    JOEL HABENER; Fiscal Year: 2004
    ..Dennis Sgroi (Massachusetts General Hospital) of a means to prepare gene expression profiling probes by Dr...
  65. Genomic Approaches to Neuronal Diversity and Plasticity
    Jingyue Ju; Fiscal Year: 2007
    ..sequencing Chip System for sequencing SAGE library from neurons; (ii) Nanoscopic DNA Arrays for global gene expression profiling at the level of individual cells and subcellular compartments, and (iii) Real-time monitoring of ..
  66. Genomic analysis of pediatric SIRS and septic shock
    Hector Wong; Fiscal Year: 2009
    ..We have been conducting gene expression profiling studies (microarray) in children with septic shock...
  67. DEVELOPMENT OF DNA MICROARRAY FABRICATION METHOD
    Maureen Cronin; Fiscal Year: 1999
    ..These arrays are well suited to simple, generic data acquisition and analysis approaches that should enable wider accessibility and broader based adoption of hybridization array based genetic analysis. ..
  68. GENOMIC ANALYSIS OF ADOLESCENT AND YOUNG ADULT ACUTE LYMPHOBLASTIC LEUKEMIA
    Cheryl L Willman; Fiscal Year: 2010
    ..performed detailed genomic characterization of standard and high risk pediatric ALL using complementary gene expression profiling, genome-wide analysis of genetic alterations, and targeted gene resequencing...
  69. Neuroendocrine Pathways Governing Energy Homeostasis
    Florence Ying Lee; Fiscal Year: 2010
    ..The Ingraham lab recently conducted global gene expression profiling studies to identify novel molecular markers for the VMH...
  70. Leukemia Signatures for Risk Classification & Targeting
    Cheryl Willman; Fiscal Year: 2009
    ..It is our hypothesis that gene expression profiling of leukemic cells will yield systematic profiles or "signatures" that can be used to improve outcome ..
  71. Gene Expression Profiling of the Kveim Siltzbach Test
    Michael Iannuzzi; Fiscal Year: 2005
    ..abstract_text> ..
  72. A Highly Multiplexed PCR Platform for Gene Expression Profiling from FFPE Tissue
    JORK N NOLLING; Fiscal Year: 2012
    ..b>Gene expression profiling has revealed that this difference in response is reflected in the biology of the tumor an two subgroups ..
  73. Preoperative and follow-up tests for thyroid tumors
    GREGORY JOSEPH RIGGINS; Fiscal Year: 2010
    ..To address this problem, we previously performed gene expression profiling both a follicular thyroid adenoma (FTA), and a follicular thyroid carcinoma (FTC)...
  74. Preoperative and follow-up tests for thyroid tumors
    Gregory Riggins; Fiscal Year: 2006
    ..To address this problem, we previously performed gene expression profiling both a follicular thyroid adenoma (FTA), and a follicular thyroid carcinoma (FTC)...
  75. Symposium on Proteomics and Toxicology
    Ian Blair; Fiscal Year: 2003
    ..Proteomics has significant advantages over gene expression profiling. Proteins can be measured reliably in a broader range of biological tissues (blood, CSF, synovial fluid, ..
  76. GENETIC ANALYSIS OF HIP FRAGILITY
    Tatiana M Foroud; Fiscal Year: 2010
    ..We plan to generate congenic rat models and conduct gene expression profiling followed by functional studies in vivo and using cultured osteoblasts and osteoclasts to identify genes ..
  77. Macaque Model and Gene Expression Profiling of SARS
    Michael Katze; Fiscal Year: 2009
    ..pathogehic;<:,, So ti signatures of SARS using global gene expression profiling. We will use humaitand;macaque using ck-oai ...
  78. Molecular Biology of Osteoarthritis
    Sergio Jimenez; Fiscal Year: 2006
    ..will examine the role of novel genes expressed in cartilage which were identified employing differential gene expression profiling on the functions of articular cartilage...
  79. Regulation of Gene Expression in Down Syndrome
    Jonathan Pevsner; Fiscal Year: 2006
    ..The specific aims are as follows: [1] Perform gene expression profiling with trisomy 21 postmortem cerebrum, cerebellum, and heart samples relative to euploid controls...
  80. Indoleamine 2, 3 dioxygenase signaling and function in Type 1 Diabetes
    Suparna Sarkar; Fiscal Year: 2009
    ..Microarray gene expression profiling of human and mouse islets exposed to a series of pro-inflammatory cytokines have revealed a remarkable ..