- 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...
- 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...
- High-resolution profiling of histone methylations in the human genome
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...
- 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...
- Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
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...
- Mapping and quantifying mammalian transcriptomes by RNA-Seq
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...
- Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
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...
- TopHat: discovering splice junctions with RNA-Seq
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...
- Differential expression analysis for sequence count data
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...
- Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
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...
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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...
- 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...
- 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...
- Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
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...
- 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...
- RNA-Seq: a revolutionary tool for transcriptomics
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...
- Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, B 9000 Ghent, Belgium
Genome Biol 3:RESEARCH0034. 2002
- MicroRNA expression profiles classify human cancers
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...
- 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...
- Integrative genomics viewer
James T Robinson
Nat Biotechnol 29:24-6. 2011
- 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...
- 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...
- Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
Department of Genetics, The Norwegian Radium Hospital, Montebello, N 0310 Oslo, Norway
Proc Natl Acad Sci U S A 98:10869-74. 2001
- MrBayes 3: Bayesian phylogenetic inference under mixed models
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...
- 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...
- 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...
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
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...
- 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...
- A microRNA expression signature of human solid tumors defines cancer gene targets
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...
- 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...
- A mammalian microRNA expression atlas based on small RNA library sequencing
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...
- 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...
- affy--analysis of Affymetrix GeneChip data at the probe level
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...
- Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
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...
- 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...
- 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...
- NCBI GEO: archive for functional genomics data sets--10 years on
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/...
- 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...
- The transcriptional landscape of the yeast genome defined by RNA sequencing
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...
- 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...
- lumi: a pipeline for processing Illumina microarray
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...
- 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...
- 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...
- qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data
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...
- 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...
- 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...
- DAVID: Database for Annotation, Visualization, and Integrated Discovery
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...
- 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/...
- DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
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...
- 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...
- 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...
- Unique microRNA molecular profiles in lung cancer diagnosis and prognosis
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...
- BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology VIB, Ghent University, Technologiepark 927, B 9052, Ghent, Belgium
Bioinformatics 21:3448-9. 2005
- MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
Max Planck Institute for Molecular Plant Physiology, Golm, Germany
Plant J 37:914-39. 2004
- Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
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...
- 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...
- 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...
- 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
- The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
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...
- The microRNA.org resource: targets and expression
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...
- 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
- ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
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...
- 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
- 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...
- 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...
- GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
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...
- WGCNA: an R package for weighted correlation network analysis
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...
- An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
Nat Genet 40:499-507. 2008
- 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...
- 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...
- MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer
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...
- 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...
- microRNA-directed phasing during trans-acting siRNA biogenesis in plants
Center for Gene Research and Biotechnology, Oregon State University, Corvallis, Oregon 97331, USA
Cell 121:207-21. 2005
- TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
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...
- Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
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...
- Identification of novel transcripts in annotated genomes using RNA-Seq
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...
- 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...
- 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
- Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
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...
- Identification of stem cells in small intestine and colon by marker gene Lgr5
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...
- NCBI GEO: archive for high-throughput functional genomic data
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/...
- Computation for ChIP-seq and RNA-seq studies
Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA
Nat Methods 6:S22-32. 2009
- A gene expression atlas of the central nervous system based on bacterial artificial chromosomes
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...
- 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...
- ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
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...
- Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
Nat Genet 41:1350-3. 2009
- The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
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...
- 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...
- 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
- 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...
- Comparing de novo assemblers for 454 transcriptome data
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...
- 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...
- 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...
- 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...
- Human induced pluripotent stem cells free of vector and transgene sequences
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...
- 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 ..
- 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...
- RNA-Seq gene expression estimation with read mapping uncertainty
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...
- Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
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...
- 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...
- 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...