We study the application of word embeddings to generate semantic representations for the domain adaptation problem of relation extraction (RE) in the tree kernel-based method. We systematically evaluate various techniques to generate the semantic representations and demonstrate that they are effective to improve the generalization performance of a tree kernel-based relation extractor across domains (up to 7% relative improvement). In addition, we compare the tree kernel-based and the feature-based method for RE in a compatible way, on the same resources and settings, to gain insights into which kind of system is more robust to domain changes. Our results and error analysis shows that the tree kernel-based method outperforms the feature-based approach.