differential expression for rna sequencing rna seq data mapping summarization statistical analysis and experimental design
Báo cáo y học: "A scaling normalization method for differential expression analysis of RNA-seq data" pps
Ngày tải lên :
09/08/2014, 20:21
... Additional file 1) However, there are sequencing- based datasets that have quite similar RNA outputs and may not need a significant adjustment For example, the small -RNA- seq data from Kuchenbauer et al ... gene expression arrays Genome Res 2008, 18:1509-1517 Bullard JH, Purdom EA, Hansen KD, Durinck S, Dudoit S: Statistical inference in mRNA -Seq: exploratory data analysis and differential expression ... Environment for Statistical Computing 2009 Robinson MD, McCarthy DJ, Smyth GK: edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics...
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Báo cáo y học: "Gene ontology analysis for RNA-seq: accounting for selection bias" pdf
Ngày tải lên :
09/08/2014, 20:21
... preparation and data analysis was designed to maximize the similarity between the microarray and RNA- seq experiments (see Marioni et al [21]) Differential expression between kidney and liver was ... identified by RNA- seq data that overlap with the microarray GO analysis are shown as a function of the number of categories selected RNAseq data have been analyzed using GOseq and hypergeometric ... results of GOseq and the standard test to the GO analysis from a microarray experiment that does not show any gene length bias [5] For the comparison of RNA- seq and microarrays, a data set was...
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Báo cáo y học: " Global and unbiased detection of splice junctions from RNA-seq data" pptx
Ngày tải lên :
09/08/2014, 20:21
... other parameters The RNA- seq data in this experiment is not strand specific, and therefore, all junction reads from both strands were combined in the RNA- MATE output All RNA- MATE exon boundaries ... small insertions and deletions In this study, we evaluated our method on public RNA- seq data from single mouse oocytes [6], sequenced on the SOLiD platform The analysis was performed on two independent ... strategy for high-throughput RNAsequencing data Bioinformatics 2009, 25:2615-2616 Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA: mRNA-Seq...
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Báo cáo y học: "Modeling non-uniformity in short-read rates in RNA-Seq data" ppt
Ngày tải lên :
09/08/2014, 20:22
... standing for different tissues, groups, or cell lines, and in total we have eight sub-datasets: three (tissues) for Wold data, three (groups) for Burge data, and two (cell lines) for Grimmond data ... of RNA- Seq Conclusions Non-uniformity is dramatic in RNA- Seq data In each of the eight sub-datasets, the RNA- Seq count data are largely over-dispersed This is strong evidence that the non-uniformity ... quantitative analysis of RNASeq data should incorporate sequencing preference information Particularly, we suggest training a model for sequencing preference using only the top 100 genes and MART,...
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Báo cáo khoa học: Differential expression pattern of the novel serine⁄threonine kinase, STK33, in mice and men doc
Ngày tải lên :
16/03/2014, 23:20
... The insert was checked for proper orientation by restriction analysis and confirmed by sequencing with standard vector primers Transformation of E coli JM109 and bacterial expression of the biotinylated ... v formamide Nonhybridized RNA was digested with RNaseA and T1 (Roche) RNA RNA hybrids were detected with antidigoxigenin Fab fragments conjugated to alkaline phosphatase (Roche) Hybridized RNA ... 4% paraformaldehyde–NaCl ⁄ Pi for 10 prior to immunohistochemistry RNA in situ hybridization Templates for the production of sense and antisense RNAs were produced by adding T7 viral RNA polymerase...
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Báo cáo khoa học: Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon a-induced early antiviral signalling pdf
Ngày tải lên :
23/03/2014, 03:20
... only component that both augments and accelerates antiviral gene expression This was confirmed by in silico analysis simulating IRF9 overexpression and subsequently experimentally validated (Fig 3A,B) ... 4748 analysis of mechanisms that determine signalling speed and the extent of pathway activation The model was used to design experiments that would be most informative, and the experimental data ... Hauser and Didier ¨ ´ ´ ´ Trono (Ecole polytechnique federale de Lausanne EPFL, Lab of virology and genetics, Switzerland) for 4752 the supplied reagents We thank Sandra Manthey and Maria Saile for...
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Báo cáo y học: " EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data" pps
Ngày tải lên :
14/08/2014, 21:20
... Workflow for web-based analysis of large genome and epigenome datasets Workflow for web-based analysis of large genome and epigenome datasets This figure outlines a workflow for the analysis ... [47] for statistical analysis and diagram generation, and the Weka package [48] for machine learning and prediction analysis The relational database stores EpiGRAPH's default attributes Oracle Database ... useful for researchers developing new bioinformatic methods for genome analysis, such as new flavors of the statistical analysis, diagram generation, machine learning analysis and prediction analysis, ...
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Power converter control circuits for two mass vibratory conveying system with electromagnetic drive simulations and experimental results IEEE trans
Ngày tải lên :
03/01/2014, 19:16
... motivation for mathematical model formulation and for further research of both the phase angle control and switch mode control behavior for the electromagnetic vibratory conveying drive Simulations and ... mains voltage zero-cross and phase shifted for angle and Simulation results for phase angles are shown in Fig 9(a) and (b), respectively Characteristic ´ ´ DESPOTOVIC AND STOJILJKOVIC: POWER ... VI EXPERIMENTAL RESULTS In this section, some experimental results are presented These results are recorded on the real experimental control systems for the SCR and transistor power converter for...
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Design, analysis, and experimental verification of continuous media retrieval and caching strategies for network based multimedia services
Ngày tải lên :
17/09/2015, 17:17
... out design, analysis, and experimental verification of retrieval and caching strategies for CM data to improve the quality of service Requested CM documents are retrieved from the server for the ... Performance comparison between GIC and GIC+ (λ = 0.25s−1 and P = 80%) 86 4.15 Performance comparison between GIC and GIC+ (B = 500M B and P = 80%) 87 4.16 Performance comparison between GIC and ... hashed part is cached data and the blank part is uncached data L When t=t1, an interval is formed by stream and stream2 In RBC, a certain amount of cache bandwidths are reserved for stream2 when t=t1...
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Design, analysis and experimental verification of tubular spaceframe chassis for FSAE application
Ngày tải lên :
12/10/2015, 17:36
... 283 284 285 286 287 Appendices 6- Data Acquisition on the Operation load of Chassis – Acquired Data 1) Skid pad Event Graph 70- Lateral, associated longitudinal and vertical acceleration experienced ... 2) Acceleration and Brake Test Graph 75-Longitudinal, associated lateral and vertical acceleration experienced by the front left unsprung mass of the race car during acceleration and brake test ... associated lateral and vertical acceleration experienced by the front right unsprung mass of the race car during acceleration and brake test 294 Graph 77-Longitudinal, associated lateral and vertical...
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Design, analysis and experimental verification of tubular spaceframe chassis for FSAE application 1
Ngày tải lên :
12/10/2015, 17:36
... stiffness (STS) of chassis 10 with respect to variation of height of rear bulkhead 229 Appendices - Design & Analysis of Chassis – Orientation of Brace 1) Chassis 11 24.80 Weight of Chassis vs Brace Variation ... 248 Figure 173-Investigation of driver ergonomics requirement of chassis 23 249 Appendices - Design & Analysis of Chassis – Cross Section of Structural Element 1) Chassis 24 Weight of Chassis (kg)...
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09 handbook of statistical analysis and data mining fixed
Ngày tải lên :
22/05/2016, 16:24
... and organizations are being forced to use statistical analysis and data mining applications in a format that combines art and science–intuition and expertise in collecting and understanding data ... 56 Data Transformation 57 Data Imputation 59 Data Weighting and Balancing 62 Data Filtering and Smoothing 64 Data Abstraction 66 Data Reduction 69 Data Sampling 69 Data Discretization 73 Data ... the historical and theoretical background for statistical analysis and data mining, and integrates it with the data discovery and data preparation operations necessary to prepare for modeling Part...
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Báo cáo y học: "ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data" doc
Ngày tải lên :
09/08/2014, 23:20
... eminent platform for analysis of gene expression and RNA processing [1-3] However, processing the raw sequence data to get useful and accurate information about gene expression and RNA processing ... gene expression data Brad A Friedman1,2,3* and Tom Maniatis4 Abstract RNA- Seq and microarray platforms have emerged as important tools for detecting changes in gene expression and RNA processing ... sequencing data and processed files (roughly to GB per lane) In short, ExpressionPlot is a unified solution for gene expression analysis of RNA- Seq and microarray data © 2011 Friedman and Maniatis;...
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Báo cáo y học: " Cloud-scale RNA-sequencing differential expression analysis with Myrna" pps
Ngày tải lên :
09/08/2014, 20:22
... W: Differential expression analysis for sequence count data Nat Precedings 2010 Baldi P, Long AD: A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical ... run only once, and the Align through Post-process stages can be re-run for subsequent analyses Discussion Myrna is a computational pipeline for RNA- Seq differential expression analysis using ... Oshlack A: A scaling normalization method for differential expression analysis of RNA- seq data Genome Biol 2010, 11:R25 Illumina Announces HiSeq(TM) 2000 Sequencing System [http://investor illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1374339]...
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Báo cáo y học: "Improving RNA-Seq expression estimates by correcting for fragment bias" doc
Ngày tải lên :
09/08/2014, 22:24
... S, Bähler J: RNA- Seq: from technology to biology Cellular and Molecular Life Sciences 2010, 67:569-579 Jiang H, Wong W: Statistical inferences for isoform expression in RNASeq Bioinformatics 2009, ... long Gel cutout sequencing sense RNA sequence paired-end read mapping anti-sense Figure Overview of a typical RNA- Seq experiment RNA is initially fragmented (1) followed by first-strand synthesis ... junctions from paired-end RNA- Seq data by SpliceMap Nucleic Acids Research 2010, 38:4570-4578 Anders S, Hüber W: Differential expression analysis for sequence count data Genome Biology 2010, 11:R106...
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Báo cáo khoa học: Design of expression vectors for RNA interference based on miRNAs and RNA splicing potx
Ngày tải lên :
07/03/2014, 11:20
... guidelines for selecting highly effective siRNA sequences [20] The oilgos for candidate sequences also contained cohesive ends for our simplified cloning strategy The artificial miRNA sequences and predicted ... splicing sequences for the miRNA expression cassette is a successful general strategy for improving marker gene protein expression In this study, insertion of the miRNA-based artificial miRNA expression ... This design mimics the structure and processing of some natural miRNAs C D Fig Strategy for improved RNAi knockdown and ⁄ or marker gene expression (A,B) In the original miRNA-based artificial miRNA...
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Báo cáo y học: "Differential expression analysis for sequence count data" ppt
Ngày tải lên :
09/08/2014, 22:23
... [http://www-huber.embl.de/users/anders/HTSeq/] 36 DESeq [http://www-huber.embl.de/users/anders/DESeq] doi:10.1186/gb-2010-11-10-r106 Cite this article as: Anders and Huber: Differential expression analysis for sequence ... than that of DESeq for weakly expressed genes and higher for strongly expressed genes As a consequence, as we have seen in Figure 2edgeR is anti-conservative for lowly DESeq allows analysis of experiments ... such an analysis with the fly RNA- Seq and the neural cell Tag -Seq data, by restricting both data sets to only two samples, one from each condition For the neural cell data, the estimated variance...
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Báo cáo y học: "Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads" pptx
Ngày tải lên :
09/08/2014, 22:23
... alignment and mapping steps of the MMSEQ workflow Table MMSEQ estimates for H13 and Mcts2 isoforms in F1 hybrid samples MMSEQ estimates for each haplotype and isoform of H13 and Mcts2 of the initial and ... Prediction of alternative isoforms from exon expression levels in RNA- Seq experiments Nucleic Acids Res 2010 Jiang H, Wong WH: Statistical inferences for isoform expression in RNASeq Bioinformatics 2009, ... estimates and the deconvolved estimates was 0.96 and 0.98, showing MMSEQ is capable of disaggregating the expression from paternal and maternal isoforms (Additional file 8) To test whether MMSEQ is...
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báo cáo khoa học: " From RNA-seq to large-scale genotyping genomics resources for rye (Secale cereale L.)" pot
Ngày tải lên :
11/08/2014, 11:21
... genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005, 21(9):1859-1875 Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping ... independent sequencing runs produced between 364,343 and 681,787 reads corresponding to ~87 and ~166 Mb of raw data per inbred line (Table 1) Subsequent quality filtering and removal of sequencing ... increased sequencing throughput and the decreasing costs, NGS technologies pave the way for sequencing even large genomes [47-49] Although of major importance for research and breeding, sequence...
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A dynamic programming algorithm for RNA structure
Ngày tải lên :
12/01/2014, 22:07
... been introduced both for RNA single-sequence folding and for RNA structural alignment and structural similarity searches The Inside and CYK dynamic programming algorithms used for SCFGbased structural ... several known RNAs (ten Dam et al., 1992) For example, by comparative analysis, RNA pseudoknots are conserved in ribosomal RNAs, the catalytic core of group I introns, and RNase P RNAs Plausible ... comparative analysis (ÁG À9 kcal/mol for sequence pattern I (32)) As expected, MFOLD predicts only one of the two stems (ÁG À7.5 kcal/mol for the same sequence) Viral RNAs Some virus RNA genomes...
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