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Gene function discovery is an important and interesting problem in computational analysis of microarray data. In this paper, we investigate the use of a semi-supervised learning algorithm for inferring gene functional classifications from heterogeneous data set consisting of DNA microarray expression measurements and phylogenetic profiles from whole-genome sequence compassions. The semisupervised learning approach aims at minimizing the disagreement between individual models built from each separate information source by employing a co-updating method and making use of both labeled and unlabeled data. Our results suggest that the semisupervised approach could be used for gene functional classification. The data sets and the program code used for the experiments can be accessed from our webpage.