SMAGEXP (Statistical Meta-Analysis for Gene EXPression) for Galaxy is a Galaxy tool suite providing a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. It handles microarray data from Gene Expression Omnibus (GEO) database or custom data ...
However, ChIP-PCR analysis did not confirm their specificity: no unique peaks were found among randomly selected top-score nutlin3a-only peaks, whereas merely 40% of RITA-only peaks were confirmed as being specific (data not shown). Moreover, microarray analysis showed that the expression of ...
Moreover, these expression 'cassettes' do not require precision in the analysis of individual gene expression, but rely on the 'consensus' expression (either up or down) of large gene sets. This primary principle of genome-wide expression profiling, that data from comprehensive sets of gene ...
The Drosophila wing disc has been a fundamental model system for the discovery of key signaling pathways and for our understanding of developmental processes. However, a complete map of gene expression in this tissue is lacking. To obtain a gene expressi
expression analysis of both gene family members reflect their preferential seed-specific expression, especially during the mature embryo development stage. Furthermore, someKCSandELOgenes were found to be specifically expressed under heat stress, phosphorus starvation, andXanthomonas campestrisinfection. The ...
However, this approach does (1) allow analysis of metagenomic sequences in protein space, overcoming issues of high-stringency read mapping relative to nucleotide reference databases (see below), and (2) allow inclusion of protein variant models, rRNA mutation models, and protein over-expression ...
(Buljan and Bateman2009; Forslund et al.2011; Wu et al.2012; Gabaldón and Koonin2013). Homolog identification forms the basis for many downstream analyses in genome exploration such as analysis of trait and gene correlation, gene expression, gene functional mutation, gene ontology-based functional...
Gene expression analysis Trimmed reads for each of the five tissues were mapped on the annotated transcriptome with the RNA-seq mapping tool of the CLC Genomics Workbench v.9.5 (Qiagen, Hilden, Germany) using the following parameters: length fraction: 0.75; similarity fraction: 0.98; maximum numbe...
Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathema
Figure 5: Analysis of the correlation of gene expression between biological replicates. Pairwise scatter plots of log2-transformed FPKM values and correlation coefficients for biological replicates of (a) MOE, (b) VNO, and (c) OB samples. Pearson correlation coefficients (r) for each comparison ...