This course provides user training for GenomatixSuite, which is a set of databases and tools for analysis of transcriptional regulatory regions. Genomatix is used via www, and it includes the data and tools to detect transcription factor binding sites and promoter modules (composite regulatory elements), to predict and retrieve promoter sequences, and to perform literature mining on gene relationships. Finnish academic researchers can obtain full access to GenomatixSuite via licensing subsidized by CSC. The course consists of lectures and hands-on sessions, and the instructor is Dr Martin Seifert from Genomatix. The tutorials illustrate the usage and interconnectivity of the different tools, and include multievidence strategies for analysis of microarray data. The following steps and tools are covered:

• retrieving promoters (Gene2Promoter, Eldorado)
• framework analysis (FrameWorker)
• database search with frameworks (ModelInspector)
• optimizing the framework model (fastM)
• data mining for gene relationships from literature (BiblioSphere)

Course material:

The course was recorded and the videos are available for viewing over the net with Real Player for registered Genomatix users. The slides and exercises are available for download:

• Introduction to gene regulation and Genomatix tools (slides)
• Multievidence strategy for microarray data analysis (slides)
• Tutorial and step by step example (pdf, gene lists used: 1, 2, 3).