Gene expression data clustering is an important biological process in DNA microarray analysis. Although there have been many clustering algorithms for gene expression analysis, finding a suitable and effective clustering algorithm is always a challenging problem due to the heterogeneous nature of gene profiles. Minimum Spanning Tree (MST) based clustering algorithms have been successfully employed to detect clusters of varying shapes and sizes. This paper proposes a novel clustering algorithm using Eigenanalysis on Minimum Spanning Tree based neighborhood graph (E-MST). As MST of a set of points reflects the similarity of the points with their neighborhood, the proposed algorithm employs a similarity graph obtained from k' rounds of MST (k'-MST neighborhood graph). By studying the spectral properties of the similarity matrix obtained from k'-MST graph, the proposed algorithm achieves improved clustering results. We demonstrate the efficacy of the proposed algorithm on 12 gene expression datasets. Experimental results show that the proposed algorithm performs better than the standard clustering algorithms. © 2016 Elsevier Ltd.