Abstract : This paper discusses different approaches for integrating biological knowledge in gene expression analysis. Indeed we are interested in the ﬁfth step of microarray analysis procedure which focuses on knowledge discovery via interpretation of the microarray results. We present a state of the art of methods for processing this step and we propose a classiﬁcation in three facets: prior or knowledge-based, standard or expression-based and co-clustering. First we discuss brieﬂy the purpose and usefulness of our classiﬁcation. Then, following sections give an insight into each facet. We summarize each section with a comparison between remarkable approaches.