Transcriptome assembly and differential gene expression analysis
De novo transcriptome assembly, functional annotation and differential gene expression analysis of juvenile and adult E. fetida, a model oligochaete used in ecotoxicological studies
... novo transcriptome assembly of ...generated transcriptome file and the trans- decoder generated peptide sequence file along with BLASTX, BLASTP and HMMER searches and were loaded into a Sqlite3 ...
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Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout
... by transcriptome information that will enhance genome assembly and ...Previously, transcriptome reference sequences were reported using data from different ...well-annotated transcriptome is ...
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DECODE: An integrated differential co-expression and differential expression analysis of gene expression data
... ( Differential Co-expression and Differential Expression) to integrate DC and DE analyses of gene expression ...in expression and co-expression are systematically ...
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A gene expression microarray for Nicotiana benthamiana based on de novo transcriptome sequence assembly
... involve assembly of the transcriptome, with or without the refer- ence genome information, gene discovery and expression analysis, identification of unknown exon junctions and ...
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Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease
... nal transcriptome study of 29 Lyme disease patients (and 13 matched controls) enrolled at the time of diagnosis and followed for up to 6 ...The differential gene expression signature of Lyme ...
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Differential Gene Expression
... Differential gene transcription is critical in ...of gene expression, one needs to use procedures that locate a particular type of messenger RNA or protein within a ...Cre-lox analysis ...
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Differential gene expression is not required for facultative sex allocation : a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis
... of differential expression between treatment groups from some genes may be obscured simply because the regulation occurs in a single tissue or group of cells and the difference in expression is ...
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Assembly and analysis of the miscanthus ?? giganteus transcriptome
... bicolor gene models was examined under the RP methodology, effectively creating individual compilations of active expression information within each Miscanthus tissue when compared to the rest of the ...
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Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection
... host gene expression profiles after H5N1 virus infection, have revealed a general phenomenon, whereby IFN and chemokine pathways are significantly up-regulated in lungs after H5N1 virus ...induced ...
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Transcriptome And Expression Profiling Analysis Link Patterns Of Gene Expression To Antennal Responses In Spodoptera Litura
... use transcriptome and expression profiling analysis to characterize the antennal transcriptome of the noctuid moth and polyphagous pest Spodoptera ...their expression levels in both ...
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Gene expression analysis and transcriptome evolution in apomicts: a case study in Boechera and Ranunculus
... the analysis of the microarray data, whereby transcriptomic expression levels throughout ovule development were compared between sexuals and ...in expression patterns throughout development. ...
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Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing
... measure gene expression, often to ask the question of what genes are differentially expressed across various biological ...determine differential expression, and have traditionally be divided ...
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Overcoming the Common Challenges in Differential Gene Expression Analysis Studies
... our analysis we see that the performance of the classifiers are sensitive to the choice of the cutoff for the truncation and that different underlying distributions require different values for the truncation in ...
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Multicriteria Gene Screening for Analysis of Differential Expression with DNA Microarrays
... Keywords and phrases: bioinformatics, gene filtering, gene profiling multiple comparisons, familywise error rates. 1. INTRODUCTION Since Watson and Crick discovered DNA more than fifty years ago, the field ...
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Statistical Methods for Gene Differential Expression Analysis of RNA-Sequencing
... depicted in Supplementary Figure 2a,b was used to benchmark different parameters. In (a), three different normalization methods: transcript counts, size factor normalization from DESEq2, and transcript-per-million (TPM) ...
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Transcriptome-Level Signatures in Gene Expression and Gene Expression Variability during Bacterial Adaptive Evolution
... in gene expression levels but also by shifts in gene expression ...variability. Gene expression variability analysis is emerging as a powerful method, particularly in ...
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edger: differential expression analysis of digital gene expression data User s Guide
... the gene varies between replicate RNA ...of differential expression in RNA-Seq ...each gene varies between replicate RNA sam- ples in such a way that the genewise standard deviations are ...
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Statistical and Computational Methods for Differential Expression Analysis in High-throughput Gene Expression Data
... quantitative analysis of alternative splicing events (referred as “pooled dataset” below), and then used an exon-based method similar to MATS in their analysis and detected 212 significantly differentially ...
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In silico analysis of the coffee transcriptome : identification of SNPs and inference of mechanisms of gene expression regulation
... EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora Jorge Maurício Costa Mondego 1, *, Ramon Oliveira Vidal 2, *, Marcelo ...
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Transcriptome analysis of murine thymocytes reveals age-associated changes in thymic gene expression
... in expression levels at all ...their expression in thymocytes with ...array analysis. Moreover, Western blot analysis of thymo- cyte lysates also confirmed that IgM increases with age (Figure ...
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