RNA-seq and microarray complement each other in transcriptome profiling

[1]  Richard A. Levine,et al.  Journal of Computational and Graphical Statistics , 2014 .

[2]  Milkha M. Leimena,et al.  Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies , 2012, Applied and Environmental Microbiology.

[3]  W. Hol,et al.  The type II secretion system: biogenesis, molecular architecture and mechanism , 2012, Nature Reviews Microbiology.

[4]  D. Rasko,et al.  Analysis of Global Transcriptional Profiles of Enterotoxigenic Escherichia coli Isolate E24377A , 2012, Infection and Immunity.

[5]  S. Burgess,et al.  RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336” , 2012, Genome Biology.

[6]  Sandrine Dudoit,et al.  GC-Content Normalization for RNA-Seq Data , 2011, BMC Bioinformatics.

[7]  A. Conesa,et al.  Differential expression in RNA-seq: a matter of depth. , 2011, Genome research.

[8]  Zhong Wang,et al.  Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.

[9]  Leming Shi,et al.  Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys. , 2011, Chemical research in toxicology.

[10]  H. Steven Wiley,et al.  Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling , 2011, Bioinform..

[11]  Mingyao Li,et al.  RNA-sequence analysis of human B-cells. , 2011, Genome research.

[12]  S. Letovsky,et al.  Protocol Dependence of Sequencing-Based Gene Expression Measurements , 2011, PloS one.

[13]  Jeffery B. Jones,et al.  HrpG and HrpX play global roles in coordinating different virulence traits of Xanthomonas axonopodis pv. citri. , 2011, Molecular plant-microbe interactions : MPMI.

[14]  M. Schell,et al.  Elucidation of the Regulon and cis-Acting Regulatory Element of HrpB, the AraC-Type Regulator of a Plant Pathogen-Like Type III Secretion System in Burkholderia pseudomallei , 2011, Journal of bacteriology.

[15]  Thomas Rattei,et al.  Effective—a database of predicted secreted bacterial proteins , 2010, Nucleic Acids Res..

[16]  B. Graveley.  The developmental transcriptome of Drosophila melanogaster , 2010, Nature.

[17]  J. Einasto.  Dark Matter , 2011, Brazilian Journal of Physics.

[18]  David R. Kelley,et al.  Quake: quality-aware detection and correction of sequencing errors , 2010, Genome Biology.

[19]  U. Bonas,et al.  Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria. , 2010, The New phytologist.

[20]  Yude Yu,et al.  The next-generation sequencing technology and application , 2010, Protein & Cell.

[21]  A. Ciccodicola,et al.  Uncovering the Complexity of Transcriptomes with RNA-Seq , 2010, Journal of biomedicine & biotechnology.

[22]  T. Hughes,et al.  Most “Dark Matter” Transcripts Are Associated With Known Genes , 2010, PLoS biology.

[23]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[24]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[25]  U. Bonas,et al.  Regulation and secretion of Xanthomonas virulence factors. , 2010, FEMS microbiology reviews.

[26]  Michael P. Snyder,et al.  RNA‐Seq: A Method for Comprehensive Transcriptome Analysis , 2010, Current protocols in molecular biology.

[27]  A. H. V. van Vliet.  Next generation sequencing of microbial transcriptomes: challenges and opportunities. , 2010, FEMS microbiology letters.

[28]  B. Simmons,et al.  A single-base resolution map of an archaeal transcriptome. , 2010, Genome research.

[29]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[30]  Frank F White,et al.  The type III effectors of Xanthomonas. , 2009, Molecular plant pathology.

[31]  J. Bähler,et al.  Cellular and Molecular Life Sciences REVIEW RNA-seq: from technology to biology , 2022 .

[32]  G. Chillemi,et al.  Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences. , 2009, New biotechnology.

[33]  A. Oshlack,et al.  Transcript length bias in RNA-seq data confounds systems biology , 2009, Biology Direct.

[34]  E M Rubin,et al.  Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing , 2009, Proceedings of the National Academy of Sciences.

[35]  Pornpimol Charoentong,et al.  ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks , 2009, Bioinform..

[36]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[37]  A. Furutani,et al.  Identification of novel type III secretion effectors in Xanthomonas oryzae pv. oryzae. , 2009, Molecular plant-microbe interactions : MPMI.

[38]  T. Harkins,et al.  Transcriptome sequencing of the Microarray Quality Control (MAQC) RNA reference samples using next generation sequencing , 2009, BMC Genomics.

[39]  P. Khaitovich,et al.  BMC Genomics BioMed Central Methodology article Estimating accuracy of RNA-Seq and microarrays with proteomics , 2022 .

[40]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[41]  R. Vossen,et al.  Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms , 2008, Nucleic acids research.

[42]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[43]  Marcel H. Schulz,et al.  A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.

[44]  J. Shendure.  The beginning of the end for microarrays? , 2008, Nature Methods.

[45]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[46]  I. Goodhead,et al.  Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution , 2008, Nature.

[47]  M. Gerstein,et al.  The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.

[48]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[49]  Chaozu He,et al.  Pghaxc and Pghbxc, Are Regulated by Type Iii Secretion Regulators Hrpx and Hrpg and Are Required for Virulence , 2022 .

[50]  D. Stokes,et al.  Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals. , 2008, Journal of structural biology.

[51]  B. Shen,et al.  cDNA cloning and function analysis of two novel erythroid differentiation related genes , 2001, Science in China Series C: Life Sciences.

[52]  A. Yakovlev,et al.  How high is the level of technical noise in microarray data? , 2007, Biology Direct.

[53]  G. Cornelis,et al.  The type III secretion injectisome , 2006, Nature Reviews Microbiology.

[54]  U. Bonas,et al.  Specific Binding of the Xanthomonas campestris pv. vesicatoria AraC-Type Transcriptional Activator HrpX to Plant-Inducible Promoter Boxes , 2006, Journal of bacteriology.

[55]  Krishanu Mukherjee,et al.  MEKHLA, a Novel Domain with Similarity to PAS Domains, Is Fused to Plant Homeodomain-Leucine Zipper III Proteins1[W] , 2006, Plant Physiology.

[56]  Frank Thieme,et al.  Type III effector proteins from the plant pathogen Xanthomonas and their role in the interaction with the host plant. , 2006, Journal of plant physiology.

[57]  Z. Szallasi,et al.  Reliability and reproducibility issues in DNA microarray measurements. , 2006, Trends in genetics : TIG.

[58]  Vincent J Carey,et al.  Bioconductor: an open source framework for bioinformatics and computational biology. , 2006, Methods in enzymology.

[59]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[60]  M. A. Machado,et al.  Expression Profiling of Virulence and Pathogenicity Genes of Xanthomonas axonopodis pv. citri , 2005, Journal of bacteriology.

[61]  Dan V. Nicolau,et al.  Microarray technology and its applications , 2005 .

[62]  A. Collmer,et al.  EFFECTOR PROTEINS : Double Agents in Bacterial Disease and Plant Defense , 2004 .

[63]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[64]  R. Lempicki,et al.  Evaluation of gene expression measurements from commercial microarray platforms. , 2003, Nucleic acids research.

[65]  Jung-Gun Kim,et al.  Characterization of the Xanthomonas axonopodis pv. glycines Hrp Pathogenicity Island , 2003, Journal of bacteriology.

[66]  Kathleen Marchal,et al.  MARAN: Normalizing Micro-array Data , 2003, Bioinform..

[67]  David Venet,et al.  MatArray: a Matlab toolbox for microarray data , 2003, Bioinform..

[68]  E. C. Teixeira,et al.  Comparison of the genomes of two Xanthomonas pathogens with differing host specificities , 2002, Nature.

[69]  Frank Thieme,et al.  Two Novel Type III-Secreted Proteins of Xanthomonas campestris pv. vesicatoria Are Encoded within the hrp Pathogenicity Island , 2002, Journal of bacteriology.

[70]  Susumu Goto,et al.  The KEGG databases at GenomeNet , 2002, Nucleic Acids Res..

[71]  Aled M. Edwards,et al.  Unfolding of Microarray Data , 2002, J. Comput. Biol..

[72]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[73]  U. Bonas,et al.  Molecular secrets of bacterial type III effector proteins. , 2001, Trends in plant science.

[74]  M. Oh,et al.  Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. , 2001, Nucleic acids research.

[75]  N. Lee,et al.  A concise guide to cDNA microarray analysis. , 2000, BioTechniques.

[76]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[77]  Y Chen,et al.  cDNA microarray technology and its applications. , 2000, Biotechnology advances.

[78]  T. Oku,et al.  Cloning and Molecular Characterization of hrpX from Xanthomonas axonopodis pv.citri , 2000, DNA sequence : the journal of DNA sequencing and mapping.

[79]  Gary A. Churchill,et al.  Analysis of Variance for Gene Expression Microarray Data , 2000, J. Comput. Biol..

[80]  R Ekins,et al.  Microarrays: their origins and applications. , 1999, Trends in biotechnology.

[81]  M Schena,et al.  Microarrays: biotechnology's discovery platform for functional genomics. , 1998, Trends in biotechnology.

[82]  G. Ramsay.  DNA chips: State-of-the art , 1998, Nature Biotechnology.

[83]  A. Collmer,et al.  The type III (Hrp) secretion pathway of plant pathogenic bacteria: trafficking harpins, Avr proteins, and death , 1997, Journal of bacteriology.

[84]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[85]  P. Lindgren.  The role of hrp genes during plant-bacterial interactions. , 1997, Annual review of phytopathology.

[86]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[87]  U. Bonas,et al.  HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria , 1996, Journal of bacteriology.

[88]  L. Penland,et al.  Use of a cDNA microarray to analyse gene expression patterns in human cancer , 1996, Nature Genetics.

[89]  U. Bonas,et al.  Sequence and expression analysis of the hrpB pathogenicity operon of Xanthomonas campestris pv. vesicatoria which encodes eight proteins with similarity to components of the Hrp, Ysc, Spa, and Fli secretion systems. , 1995, Molecular plant-microbe interactions : MPMI.

[90]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[91]  C. Kado,et al.  Conservation of the hypersensitivity-pathogenicity regulatory gene hrpX of Xanthomonas campestris and X. oryzae. , 1995, DNA sequence : the journal of DNA sequencing and mapping.

[92]  A. Collmer,et al.  Erwinia chrysanthemi and Pseudomonas syringae: plant pathogens trafficking in extracellular virulence proteins. , 1994, Current topics in microbiology and immunology.

[93]  U. Bonas.  hrp genes of phytopathogenic bacteria. , 1994, Current topics in microbiology and immunology.

[94]  S. P. Fodor,et al.  Multiplexed biochemical assays with biological chips , 1993, Nature.

[95]  C. Boucher,et al.  Conservation of secretion pathways for pathogenicity determinants of plant and animal bacteria. , 1993, Trends in microbiology.

[96]  W. Cleveland,et al.  Regression by local fitting: Methods, properties, and computational algorithms , 1988 .

[97]  M. Daniels,et al.  Cloning of genes involved in pathogenicity of Xanthomonas campestris pv. campestris using the broad host range cosmid pLAFR1 , 1984, The EMBO journal.