Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract J-Express is a comprehensive portable software package for the analysis and visualization of microarray data.

The software gives you access to methods for unsupervised analysis (clustering etc.), supervised analysis (SAM, Feature Subset Selection, etc.) and visualization in an integrated and flexible way.

Its efficiency allows interactive clustering of thousands of expression profiles on standard personal computers.

Supervised analysis can be performed on samples by simple user- guided sample annotation or on genes through tools for metabolic pathway analysis and Gene Ontology (GO) mapping.

J-Express is compatible with data from most microarray data systems, including GenePix, Affymetrix, Agilent, Scanalyze and ArrayExpress (see G6G Abstract Number 20012) and it contains a flexible interface to manually build file readers from other sources.

Traditional tabular formatted files (e.g. MS Excel) are easily imported into J-Express. In addition, J-Express is programmed in Java which means that it can run on most operating systems, including MS Windows, Linux, Mac/OS and UNIX.

Stay updated -- New methods in microarray analysis are frequently presented by the microarray community around the world and quick implementation of these is essential for a software package.

MolMine has developed a quick update system that makes J-Express update itself as soon as new methods are developed.

MolMine data servers also provide microarray annotation for most microarrays and a dataset repository to share data between user groups (defined by the user) or to publish for the community. J-Express 2.7 - Some selected features/capabilities include:

1) Significance Analysis of Microarrays - SAM;

2) Gene Ontology (GO) Mapping and analysis;

3) Metabolic pathway analysis;

4) Clustering and projection methods;

5) ANOVA + P-values and FDR;

6) t-score and s-score testing (for tumor vs. normal 2 channel hybridizations);

7) MAGE-ML input and output.

J-Express components -- is a ‘light version’ of J-Express 2.7 (and 2.8) and it enables the user to select a subset of the methods available in the full software package. It lets the user select between several method packages (modules) to customize the functionality and reduce costs.

You may choose from the following packages (modules):

1) Low-level data preparation;

2) Significance Analysis of Microarrays - SAM;

3) Gene Set Enrichment Analysis;

4) Gene Ontology (GO) Mapping and analysis;

5) Metabolic pathway analysis;

6) Clustering and projection methods;

7) t-score and s-score testing (for tumor vs. normal 2 channel hybridizations);

8) MAGE-ML input and output.

SpotPix Suite -- is the low-level data preparation module in J-Express. It also comes as a separate analysis package and enables the compilation of gene expression matrices from multiple image analysis files.

Input is typically statistical data from single samples which can be analyzed, quality controlled, checked for artifacts such as hybridization errors, filtered and normalized.

Finally, the multiple arrays can be compiled to a single expression matrix with one gene per row and one sample per column and exported to a tab-delimited file. These files can then be imported into various data analysis packages such as Microsoft Excel for further studies.

File Types -- The SpotPix Suite comes with many file readers, including the most popular Image analysis formats for GenePix, Scanalyze, Affymetrix (text files) and Agilent. For other formats, MolMine offers an intuitive tool for building custom file parsers.

Extended interface -- A scripting interface can be used to implement new preparation processes either as simple Python (Jython) scripts or new Java code. Examples are provided for both analysis and visualization of data.

System Requirements

Contact manufacturer.


Manufacturer Web Site J-Express

Price Contact manufacturer.

G6G Abstract Number 20218

G6G Manufacturer Number 101825