Methods for Simultaneously Identifying Coherent Local Clusters with Smooth Global Patterns in Gene Expression Profiles
學年 96
學期 2
出版（發表）日期 2008-03-01
作品名稱 Methods for Simultaneously Identifying Coherent Local Clusters with Smooth Global Patterns in Gene Expression Profiles
作品名稱（其他語言）
著者 Tien, Yin-jing; Lee, Yun-shien; Wu, Han-ming; Chen, Chun-houh
單位 淡江大學數學學系
出版者 London: BioMed Central Ltd.
著錄名稱、卷期、頁數 BMC Bioinformatics 9, 155(16pages)
摘要 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 rank-two 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 expression profiles that preserves coherent local clusters and identifies global grouping trends.
 Conclusion: We demonstrate, through four examples, that the proposed method not only possesses better numerical and statistical properties, it also provides more meaningful biomedical insights than other sorting algorithms. We suggest that sorted proximity matrices for genes and arrays, in addition to the gene-by-array expression matrix, can greatly aid in the search for comprehensive understanding of gene expression structures. Software for the proposed methods can be obtained at http://gap.stat.sinica.edu.tw/Software/GAP
關鍵字
語言 en
ISSN 1471-2105
期刊性質 國外
收錄於 SCI
產學合作
通訊作者 Chen, Chun-houh
審稿制度
國別 GBR
公開徵稿
出版型式 紙本
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