Like Liam said, this sort of analysis is dependent on the database you use, which may not be adequate for what you are trying to accomplish. And as far as I know, these databases are at the gene, not isoform, level. So if a change in two conditions is a result of a change in which isoform is expressed, rather than the amount of expression, you will not detect it.
Also it treats genes as equals that are independent of each other but thats usually not the case. For example if p53, at the top of a pathway, is expressed differently, that has much stronger implications than if a gene at the bottom of the pathway was expressed differently. Additionally, it treats each pathway as independent of each other, but again that is usually not that case and there usually is some overlap between pathways.
You can read more here http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375