Pathway analysis

How to use the Pathway module of for pathway analysis of microarray data

Authors: Friederike Ehrhart, Lars Eijssen, Anwesha Bohler, Linda Rieswijk, Egon Willighagen (Maastricht University), Penny Nymark (Misvik Biology)


PathVisio and are open source, free to use online platforms for analysis of microarray data - and an alternative program for Chipster. This tutorial shows how to use the Path module (Pathway module, PathVisio webtool) of ArrayAnalysis which is designed for doing pathway analysis on microarray data. All source code has been written in R and is available at

This technical documentation has two main objectives:
to guide you in the use of the Path module
to give interpretative help on the outputs of the module

The Path module can be run :
on-line via the webportal (follow "Get started" and choose "Pathway analysis")
or as an automated R workflow from a local computer

The main functions of the Path module are:
to import a dataset;
to create a visualization;
to calculate z-scores based on the criterion;
to return a list of pathways sorted on the basis of z-scores.

How to use the documentation: As shown in the Table Of Contents, you will find the separate sections :
Using the on-line Path module
Interpreting the results provided.

Bug tracking system: If you encounter an issue by using the code, you can report it at any moment on our internal tracking system : You can also use this system to post comments or feature suggestions.

Example gene level statistics file: An example dataset is available. When running the module, you can check a box to use this data set (Example1) in order the explore the functionality of the module.

You can download the tutorial >> here << or see it in the preview window below.