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Differential gene expression and network analysis in head and neck squamous cell carcinoma
Head and neck squamous cell carcinoma (HNSCC) is a prevalent malignancy with a poor prognosis, whose biomarkers have not been studied in great...
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Gene Expression Regulation in Plant Abiotic Stress Response
This chapter extensively explores the molecular mechanisms governing gene expression in plants facing abiotic stresses, with a specific focus on...
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Differential gene expression and immune cell infiltration in maedi-visna virus-infected lung tissues
BackgroundMaedi-visna virus (MVV) is a lentivirus that infects monocyte/macrophage lineage cells in sheep, goats, and wild ruminants and causes...
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Genealyzer: web application for the analysis and comparison of gene expression data
BackgroundGene expression profiling is a widely adopted method in areas like drug development or functional gene analysis. Microarray data of gene...
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A pseudo-value regression approach for differential network analysis of co-expression data
BackgroundThe differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions....
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GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership
Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell...
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PEATmoss: A Gene Expression Atlas for Bryophytes
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data...
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Transcriptome analysis revealed differences in gene expression in sheep muscle tissue at different developmental stages
BackgroundThe analysis of differentially expressed genes in muscle tissues of sheep at different ages is helpful to analyze the gene expression...
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Differential bumble bee gene expression associated with pathogen infection and pollen diet
BackgroundDiet and parasitism can have powerful effects on host gene expression. However, how specific dietary components affect host gene expression...
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Monitoring Mechano-Regulation of Gene Expression by RNA Sequencing
The advent of high-throughput sequencing techniques has revolutionized biological research. One such method is RNA sequencing, which has become a...
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Fused inverse-normal method for integrated differential expression analysis of RNA-seq data
BackgroundUse of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application...
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Impact of human gene annotations on RNA-seq differential expression analysis
BackgroundDifferential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are...
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Differential venom gland gene expression analysis of juvenile and adult scorpions Androctonus crassicauda
BackgroundThe Androctonus crassicauda , belonging to the genus Androctonus of the family Buthidae, is the most venomous scorpion in Middle East...
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De novo transcriptome assembly and global analysis of differential gene expression of aphid tolerant wild mustard Rorippa indica (L.) Hiern infested by mustard aphid Lipaphis Erysimi (L.) Kaltenbach
Rapeseed-mustard, the oleiferous Brassica species are important oilseed crops cultivated all over the globe. Mustard aphid Lipaphis erysimi (L.)...
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Genome-Wide Expression Analysis of Genes Involved in Somatic Embryogenesis
Genome-wide expression analysis is an important tool for identifying and analysing genes involved in various biological processes, including cell...
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Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
BackgroundB-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying...
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Differential gene expression analysis of common target genes for the detection of SARS-CoV-2 using real time-PCR
COVID-19 currently is the main cause of the severe acute respiratory disease and fatal outcomes in human beings worldwide. Several genes are used as...
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Particulate matter-induced gene expression patterns in human-derived cells based on 11 public gene expression datasets
BackgroundExposure to particulate matter (PM) and house dust mite (HDM) can change the expression patterns of inflammation-, oxidative stress-, and...
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Transcriptional Regulation of Gene Expression in Plant Abiotic Stress Response
This chapter offers an in-depth analysis of gene expression regulation through transcriptional mechanisms, with a particular focus on the significant...
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Flimma: a federated and privacy-aware tool for differential gene expression analysis
Aggregating transcriptomics data across hospitals can increase sensitivity and robustness of differential expression analyses, yielding deeper...
