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Differential gene expression

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

... In recent years, rNa-Seq technologies became a powerful tool for transcriptome studies. however, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In ...

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Differential gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenic development.

Differential gene expression profiling of human bone marrow-derived mesenchymal stem cells during adipogenic development.

... decreased expression) that were differentially expressed during adipogenic development of MSC and/or between MSC and fat tissue in a highly significant way (p < ...Comparing differential gene ...

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Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression

... the gene-specific variation, they technically require at least 2 replicates per condi- ...the expression of a single ...of expression of the genes, it is necessary to transform a set of k probe ...

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Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation

Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation

... this gene in GRMD dog muscle, followed by a slight ten- dency to decreased gene expression four months after MuStem cell transplantation, which is confirmed by ...

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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

... Université de Toulouse, INRA, Castanet-Tolosan, France RNA-Seq is a widely used technology that allows an efficient genome-wide quantification of gene expressions for, for example, differential ...

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Early differential gene expression in haemocytes from resistant and susceptible Biomphalaria glabrata strains in response to Schistosoma mansoni

Early differential gene expression in haemocytes from resistant and susceptible Biomphalaria glabrata strains in response to Schistosoma mansoni

... transforming miracidia/developing sporocysts are also likely important determinants of the resistance response. Integrin-like cell surface receptors [29] are known to regulate haemocyte adhesion and motility [30–32] and ...

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Early differential gene expression in haemocytes from resistant and susceptible Biomphalaria glabrata strains in response to Schistosoma mansoni

Early differential gene expression in haemocytes from resistant and susceptible Biomphalaria glabrata strains in response to Schistosoma mansoni

... transforming miracidia/developing sporocysts are also likely important determinants of the resistance response. Integrin-like cell surface receptors [29] are known to regulate haemocyte adhesion and motility [30–32] and ...

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Statistical modelling for differential gene expression studies: variance-covariance models, sequential and meta-analysis.

Statistical modelling for differential gene expression studies: variance-covariance models, sequential and meta-analysis.

... gene expression / two colour microarray / simulation / statistical analysis ...global gene expression changes at the cellular level, allowing researchers to measure the expression of ...

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Differential gene expression according to race and host plant in the pea aphid

Differential gene expression according to race and host plant in the pea aphid

... found both a plastic response and genetically based adaptations enhancing host-associated fitness differ- ences. The pea aphid, Acyrthosiphon pisum, was the first aphid species to have its genome sequenced (The Inter- ...

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Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection

Differential gene expression of the honey bee Apis mellifera associated with Varroa destructor infection

... in gene expression For most of the genes showing significant differences in expression in the present study, the magnitude of these differences was ...underestimate gene expres- sion changes ...

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Differential miRNA-Gene Expression in M Cells in Response to Crohn’s Disease-Associated AIEC

Differential miRNA-Gene Expression in M Cells in Response to Crohn’s Disease-Associated AIEC

... and gene expression in IECs and M cells upon AIEC infection have not been ...and gene profiling under basal condition and upon infection with the reference AIEC LF82 ...Both differential ...

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Spectral analysis of gene expression profiles using gene networks

Spectral analysis of gene expression profiles using gene networks

... a gene is involved, the biologist is often more interested in the biological function than in the single ...the expression of a single gene, but involves the entire set of genes that form the ...

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Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

... Differential gene expression In Paramecium, the sexual cycle encompasses meiosis, fertilization and development of a new ...characterize differential gene expression during ...

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Chromosomal profiles of gene expression in Huntington's disease.

Chromosomal profiles of gene expression in Huntington's disease.

... For this purpose, Chromowave applied the singular value decomposition to the set of wavelet coefficients to extract the first eigenvector, e.g. the main pattern of variation. This pattern was subsequently filtered using ...

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Increasing stability and interpretability of gene expression signatures

Increasing stability and interpretability of gene expression signatures

... We assess the relevance of a new method named the graph Lasso, pro- posed recently by Jacob et al. (2009), to automatically learn such a signa- ture given a training set of expression data and a gene ...

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Control of gene expression by cell size

Control of gene expression by cell size

... downstream gene repression in the tetraploid and the cln3 ∆ ...higher expression of these genes will require more detailed computational and genetic ...

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A Multi-strategy approach to informative gene identification from gene expression data

A Multi-strategy approach to informative gene identification from gene expression data

... individual gene in the peripheral, as long as it finds a gene in the core that has similar promoter composition with a similarity score ≥ ...this gene is ...

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Unsupervised Bayesian linear unmixing of gene expression microarrays

Unsupervised Bayesian linear unmixing of gene expression microarrays

... like gene expression ...positive gene signatures, called factors, with random positive mixing coefficients, called factor scores, that specify the relative contribution of each signature to a ...

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Gene Expression Profiling of Solitary Fibrous Tumors

Gene Expression Profiling of Solitary Fibrous Tumors

... demethylation, as observed in Wilms tumors [38], warrants methylome analysis of SFT samples. Given the fact that CD34, the most consistent marker of SFT to date, is a marker of hematopoı¨etic stem cells, it was quite ...

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Deep learning benchmarks on L1000 gene expression data

Deep learning benchmarks on L1000 gene expression data

... We compare traditional classifiers, including feed-forward artificial neural net- works (FF-ANNs), linear methods, random forests, decision trees, and K nearest neighbo[r] ...

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