HAMSTER: Visualizing microarray experiments as a set of minimum spanning trees

Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka, Paul Horton

研究成果: Article同行評審

1 引文 斯高帕斯(Scopus)

摘要

Background: Visualization tools allow researchers to obtain a global view of the interrelationships between the probes or experiments of a gene expression (e.g. microarray) data set. Some existing methods include hierarchical clustering and k-means. In recent years, others have proposed applying minimum spanning trees (MST) for microarray clustering. Although MST-based clustering is formally equivalent to the dendrograms produced by hierarchical clustering under certain conditions; visually they can be quite different. Methods: HAMSTER (Helpful Abstraction using Minimum Spanning Trees for Expression Relations) is an open source system for generating a set of MSTs from the experiments of a microarray data set. While previous works have generated a single MST from a data set for data clustering, we recursively merge experiments and repeat this process to obtain a set of MSTs for data visualization. Depending on the parameters chosen, each tree is analogous to a snapshot of one step of the hierarchical clustering process. We scored and ranked these trees using one of three proposed schemes. HAMSTER is implemented in C++ and makes use of Graphviz for laying out each MST. Results: We report on the running time of HAMSTER and demonstrate using data sets from the NCBI Gene Expression Omnibus (GEO) that the images created by HAMSTER offer insights that differ from the dendrograms of hierarchical clustering. In addition to the C++ program which is available as open source, we also provided a web-based version (HAMSTER+) which allows users to apply our system through a web browser without any computer programming knowledge. Conclusion: Researchers may find it helpful to include HAMSTER in their microarray analysis workflow as it can offer insights that differ from hierarchical clustering. We believe that HAMSTER would be useful for certain types of gradient data sets (e.g time-series data) and data that indicate relationships between cells/tissues. Both the source and the web server variant of HAMSTER are available from http://hamster.cbrc.jp/.

原文English
文章編號8
期刊Source Code for Biology and Medicine
4
DOIs
出版狀態Published - 2009 十一月 20

All Science Journal Classification (ASJC) codes

  • 資訊系統
  • 電腦科學應用
  • 健康資訊學
  • 資訊系統與管理

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