Dataset Information

Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data.

ABSTRACT:

Background

One of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measure, applicable to all branches and across multiple scales of dissimilarity.

Results

We formulate a method termed Tree Branches Evaluated Statistically for Tightness (TBEST) for identifying significantly distinct tree branches in hierarchical clusters. For each branch of the tree a measure of distinctness, or tightness, is defined as a rational function of heights, both of the branch and of its parent. A statistical procedure is then developed to determine the significance of the observed values of tightness. We test TBEST as a tool for tree-based data partitioning by applying it to five benchmark datasets, one of them synthetic and the other four each from a different area of biology. For each dataset there is a well-defined partition of the data into classes. In all test cases TBEST performs on par with or better than the existing techniques.

Conclusions

Based on our benchmark analysis, TBEST is a tool of choice for detection of significantly distinct branches in hierarchical trees grown from biological data. An R language implementation of the method is available from the Comprehensive R Archive Network: http://www.cran.r-project.org/web/packages/TBEST/index.html.

SUBMITTER: Sun G

PROVIDER: S-EPMC4253613 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature

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Publications

Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data.

Sun Guoli G Krasnitz Alexander A

BMC genomics 20141119

<h4>Background</h4>One of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measure, applicable to all branches and across multiple scales of dissimilarity.<h4>Results</h4>We formulate a method termed Tree Branches Evaluated Statistically for Tightness ...[more]

PMID: 25409689

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Dataset Information

Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data.

Background

Results

Conclusions

Publications

Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data.

Similar Datasets

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