Analysis of Gene‐Expression Data Using J‐Express

Abstract

The J‐Express package has been designed to facilitate the analysis of microarray data with an emphasis on efficiency, usability, and comprehensibility. The J‐Express system provides a powerful and integrated platform for the analysis of microarray gene expression data. It is platform‐independent in that it requires only the availability of a Java virtual machine on the system. The system includes a range of analysis tools and a project management system supporting the organization and documentation of an analysis project. This unit describes the J‐Express tool, emphasizing central concepts and principles, and gives examples of how it can be used to explore gene expression data sets. Curr. Protoc. Bioinform. 21:7.3.1‐7.3.25. © 2008 by John Wiley & Sons, Inc.

Model of Tryptophan Metabolism, Readily Scalable Using Tissue-specific Gene Expression Data

“…Software Used for Analysis and Visualizations-Expression data were formatted using J-Express Pro 2012 (31,32). All calculations of fluxes and intermediate concentrations were performed with the steady state task of COPASI 4.10 (33).…”

Antileukaemic effect of PI3K‐mTOR inhibitors in acute myeloid leukaemia‐gene expression profiles reveal CDC25B expression as determinate of pharmacological effect

“…The data from the scanning of arrays on the IlluminaiScan Reader was investigated in GenomeStudio and J-Express 2012 (MolMine AS, Bergen, Norway) for quality control measures (Stavrum et al, 2008). Before being compiled into an expression profile data matrix, all arrays within each experiment were quintile normalized to be comparable.…”

“…Other bioinformatical analyses were also performed using the J-Express 2012 analysis suite (MolMine AS; Stavrum et al, 2008). Proliferation ratios were transformed to logarithmic values (base 2) before analysis, and unsupervised hierarchical clustering was performed with correlation and distance measure as described for each test.…”

The surface molecule signature of primary human acute myeloid leukemia (AML) cells is highly associated with NPM1 mutation status

“…All patients were examined with regard to the expression of CD11c (expressed on monocytes), CD13 (monocytes, neutrophils), CD14 (mainly expressed on monocytes, at lower levels on neutrophils), CD15 (mainly neutrophils, also monocytes), CD33 (appears on myelomonocytic precursors after CD34), CD34 (immature hematopoietic cells), CD45 (leukocytes) and HLA-DR. 4 The French-American-British (FAB) classification was used for morphological evaluation of the differentiation status, 5 and analysis for FLT3 and NPM-1 mutations was performed as previously described. 6 Bioinformatical analyses were performed using the J-Express 2009 analysis suite (MolMine AS, Bergen, Norway) 7 and hierarchical clustering was performed with Pearson's correlation as distance measure and complete weighted linkage. Based on the surface expression level of this limited number of differentiation markers, the patients could be classified by hierarchical clustering into distinct subsets (Figure 1).…”