This chapter aims to describe the process and use of the tools required to perform a reference-based RNA-Seq gene expression analysis using the Galaxy public web server.González-Bodí, SaraDepartamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria...
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
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 ...
We therefore examined the correlation between expression of genes containing the composite NRF-1/mH2A nucleosome and that of genes containing plain mH2A in mH2A KD cells. Figure 5A shows a co-clustering analysis demonstrating that among the 5,059 gene promoters bound by mH2A, the ones bearing...
SSH is a high throughput gene expression analysis method and its ability to identify differentially expressed genes lies on the facts that it is: irrespective of the expression level, does not require sequence information, eliminates the need for physical separation of single- and double-stranded...
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 ...
See Additional file 2: Table S9 for complete DESeq2-analysis results. Fig. S2. Influence of GSC and daf-2 status on fatty acid desaturase gene-expression. Accompanies Fig. 3. Expression levels of the genes indi‑ cated were determined in GSC(−) relative to GSC(+) (a), and...
Our analysis of microarray data containing primary and metastatic cancer samples has revealed not only differentially expressed genes, but also relations between different groups of primary and metastatic cancer. Metastatic samples tend to occupy a distinct partition of gene expression space. Further ...
L.L. performed the ChIP–seq, HiChIP–seq, RNA-seq and relevant data analysis. W.R. and J.S. assisted with the protein expression and purification. L.L. and P.W. analyzed the data. L.L. and Y.W. wrote the manuscript, which was reviewed and commented by all co-authors. ...
We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating ...