Microarray data analysis and Cytoscape Network Visualization
by Bala Gür-Dedeoğlu and Ahmet Raşit Öztürk
There are several approaches suggested for the analysis of microarray data however none of these methods is proved to be the perfect solution due to the nature of the microarray technique. Therefore, it is important to understand advantages and disadvantages of each analysis method., Main considerations about the microarray analysis approaches will be covered in the first part of this workshop and a basic approach for the data analysis will be applied with the participants.
It is possible to understand the relationship between functionally related complexes through the investigation of the transcriptional regulation and the discovery of co-regulated genes. Using the microarray data, correlation between the expression of genes for a specific condition can be easily calculated.
Further analysis and interpretation of the created network, which is known as network analysis, can be applied using the Cytoscape software (www.cytoscape.org) for the visualization of the relationships and to reveal the co-regulated genes. In the second part of the workshop, an introduction to the visual capabilities of the Cytoscape software will be shown with an example.
The database can be accessed from here.