We propose an integrative self-organizing map (iSOM) for exploring differential expression patterns across multiple microarray experiments. The algorithm is based on the assumption that observed differential expressions are random samples of a mean pattern model which is unknowna priori. The learning mechanism of iSOM is similar to the conventional SOM. The mean pattern model which underlies the proposed iSOM models mean differential expressions using a one-dimension of mean differential expressions for the mean differential expressions. The feature map of an iSOM model can be used to reveal correlation between multiple medically/biologically related disease types or multiple platform experiments for one disease. We illustrate applications of iSOM using simulated data and real data.