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[PDF] Top 20 Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes

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Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes

Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes

... years, rNa-Seq technologies became a powerful tool for transcriptome ...computational methods dedicated to the analysis of high-throughput sequencing data are yet to be ... Voir le document complet

10

Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation

Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation

... Performing RNA-Seq on samples displaying a global shift in expression The purpose of our present work was to describe genome-wide gene expression profiles from ... Voir le document complet

26

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

Optimization of an RNA-Seq Differential Gene Expression Analysis Depending on Biological Replicate Number and Library Size

... France RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential expression ... Voir le document complet

19

Gene co-expression analysis unravels a link between C9orf72 and RNA metabolism in myeloid cells

Gene co-expression analysis unravels a link between C9orf72 and RNA metabolism in myeloid cells

... list of GO terms for which a significant enrichment with an adjusted p-value < ...increase of C9orf72 mRNA levels associates with a concomitant downreg- ulation of genes that ... Voir le document complet

3

Characterization of FUS Mutations in Amyotrophic Lateral Sclerosis Using RNA-Seq

Characterization of FUS Mutations in Amyotrophic Lateral Sclerosis Using RNA-Seq

... Our analysis also identified differences between R521G and R522G FUS ...mutants. Differential expression analysis demon- strated that these mutations appeared to have opposite effects on ... Voir le document complet

9

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

... those expression regulates lung tumour pro- gression ( 28 ). Finally, a TFs cooperation subnetwork (or- ange) is functionally enriched in hormone receptor anno- tations as it contains factors, such ... Voir le document complet

15

Comparison of data-driven analysis methods for identification of functional connectivity in fMRI

Comparison of data-driven analysis methods for identification of functional connectivity in fMRI

... Data-driven methods provide an alternative to testing each voxel's time course against a hypothesis. Also known as exploratory analysis, data-driven analysis explores the mul[r] ... Voir le document complet

103

A comparison of blade tip timing data analysis methods

A comparison of blade tip timing data analysis methods

... data analysis methods presented in this work were applied to simulated data obtained from a simple mathematical model of the forced synchronous response of a rotating ... Voir le document complet

12

Gene expression analysis of flax seed development

Gene expression analysis of flax seed development

... DGAT expression in vegetative tissues is too low to detect with the EST ...results in the desirable omega-3 and omega-6 fatty acids ...spike in the number of ESTs representing the Fatty ... Voir le document complet

50

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard

... range for the ratio between internal primer and total 16S rRNA gene The efficiency of the primers pair E detecting the DNA internal standard across the serial dilutions was 90% (Figure A3), allowing ... Voir le document complet

22

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Assessing reproducibility of matrix factorization methods in independent transcriptomes

... cell of the colon) and KRAS ...B-cells. Of particular interest is the identification of the communities related to B-cells and CAFs whose association to these cell types was evident not only using ... Voir le document complet

8

A performance comparison of sensitivity analysis methods for building energy models

A performance comparison of sensitivity analysis methods for building energy models

... 11 a typical dwelling designed for low income ...has a gross floor area of 53 m 2 with two small bedrooms and is located on the 4 th floor at a corner of the building (see Figure ... Voir le document complet

30

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

Wide cross-species RNA-Seq comparison reveals a highly conserved role for Ferroportins in nickel hyperaccumulation in plants

... membrane of the ...sequestration in vacuoles. The development of RNA-Seq technologies has opened the possibility to study non-model species at the molecular ...because of the ... Voir le document complet

22

Analysis and expression of a cloned pre-T cell receptor gene

Analysis and expression of a cloned pre-T cell receptor gene

... is a multi-disciplinary open access archive for the deposit and dissemination of sci- entific research documents, whether they are pub- lished or ...institutions in France or abroad, or from ... Voir le document complet

7

Evaluation and Optimization of Clustering in Gene Expression Data Analysis

Evaluation and Optimization of Clustering in Gene Expression Data Analysis

... A new method for proper assessment of cluster quality is therefore preferred so that: (i) the data set is kept intact during clustering, (ii) one is able to determine the optimal number of ... Voir le document complet

12

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

... assembly of short reads is prone to cause artefacts and to generate false chimeric transcripts (Yang and Smith, ...corrected for instance by comparing reconstructed transcripts with transcripts/ proteins ... Voir le document complet

9

Sequence analysis of the ARG7 gene of Schizosaccharomyces pombe coding for argininosuccinate lyase. Expression of the gene in Saccharomyces cerevisiae.

Sequence analysis of the ARG7 gene of Schizosaccharomyces pombe coding for argininosuccinate lyase. Expression of the gene in Saccharomyces cerevisiae.

... The transcription initiation sites have been determined by primer extension using as a primer a 19 b oligonucle-... Northern blots of RNA prepared from S.[r] ... Voir le document complet

6

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

... end RNA-Seq methods, the vast majority of CAGE peaks have additional support ...~55% of false positive and ~42% of intergenic peaks for CAGE have support from Gencode ... Voir le document complet

29

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Comprehensive comparative analysis of strand-specific RNA sequencing methods

... Our analysis allowed us to assess the tradeoff between different protocol ...modifications. For example, we found that Actinomycin D improved the strand-specificity of the NNSR protocol ... Voir le document complet

18

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

... sequence of the chicken genome, like several other draft genome sequences, is presently not fully ...result in gene fragmentation and imprecise gene ...from RNA sequencing ... Voir le document complet

9

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