Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles

Background: The hierarchical clustering tree (HCT) with a dendrogram [1] and the singular value decomposition (SVD) with a dimension-reduced representative map [2] are popular methods for two-way sorting the gene-by-array matrix map employed in gene expression profiling. While HCT dendrograms tend to optimize local coherent clustering patterns, SVD leading eigenvectors usually identify better global grouping and transitional structures. Results: This study proposes a flipping mechanism for a conventional agglomerative HCT using a rank-two ellipse (R2E, an improved SVD algorithm for sorting purpose) seriation by Chen [3] as an external reference. While HCTs always produce permutations with good local behaviour, the ranktwo ellipse seriation gives the best global grouping patterns and smooth transitional trends. The resulting algorithm automatically integrates the desirable properties of each method so that users have access to a clustering and visualization environment for gene express...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Yin-Jing Tien, Yun-Shien Lee, Han-Ming Wu, Chun-Houh Chen
• Keywords: BMCBI 2008, Gene Expression, Global Grouping, Hierarchical Clustering Tree