Background: Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these researchers' needs by facilitating the possibility to test and formulate from a hypothesis to entire models under a holistic point of view. Results: PCOPGene-Net is a web application for facilitating the study of the relationships among gene expressions under microarray conditions, to classify these conditions and to study their effect on expression relationships. Furthermore, the system guides the researcher in the navigation through the microarray data by providing the most suitable genes and information for the researcher's interests at each moment. We achieve all of these by means of the zoom-out operation, the zoom-in operation, the non-continuous analysis and crossing the PCOPGene results with external data-servers. Conclusion: PCOPGene-Net helps to identify cellular states and the genes involved in these. All of that is accomplished in a flexible way, guided by the researcher's interests and taking advantage of the ability of our system to relate gene expressions, even when these relationships are non-continuous and cannot be found using linear or non-linear analytical methods. Currently, our tools are used for tumour-progression study from a holistic point of view. © 2009 Huerta et al; licensee BioMed Central Ltd.