ExpressionView-package: The ExpressionView package

In ExpressionView: Visualize biclusters identified in gene expression data

Description

A package designed to interactively explore biclusters identified in gene expression data.

Introduction

Clustering genes according to their expression profiles is an important task in analyzing microarray data. ExpressionView allows the user to explore the biclusters together with the underlying data in an interactive environment. The applet requires a browser with Adobe Flash player 10 installed.

The ExpressionView package can treat gene expression data in the form of a Bioconductor ExpressionSet. It recognizes biclusters identified by the Iterative Signature Algorithm (ISA) implemented in the ISA package as well as the methods available in the biclust package.

Worflow

The usual workflow consist of three steps:

Order

To arrange the possibly overlapping biclusters in a visually appealing layout, the gene expression data has to be reordered in such a way that individual biclusters from contiguous rectangles. The optimal order is found by the OrderEV function.

Export

In a second step, the biclusters and all the relevant biological information are combined and exported to an ExpressionView XML file. This is done by the ExportEV function.

Visualize

The Flash applet is started by the LaunchEV command. Video tutorials describing the various features of the applet can be found on the ExpressionView website (http://www.unil.ch/cbg/ExpressionView).

A tutorial can be found in the accompanying vignette of the package.

Biclustering with non-gene expression data

Both, the ISA and the biclustering methods implemented in the biclust package can treat any two-dimensional data, i.e., not necessarily originating from gene expression profiling. While the ExpressionView package is optimized for gene expression matrices, it is also possible to explore data stemming from other sources. For more information, see the description of the ExportEV function.

Author(s)

Andreas Lüscher [e-mail]

See Also

OrderEV, ExportEV and LaunchEV

ExpressionView documentation built on Nov. 8, 2020, 8:26 p.m.