Dataset Information

Revealing functionally coherent subsets using a spectral clustering and an information integration approach.

ABSTRACT:

Background

Contemporary high-throughput analyses often produce lengthy lists of genes or proteins. It is desirable to divide the genes into functionally coherent subsets for further investigation, by integrating heterogeneous information regarding the genes. Here we report a principled approach for managing and integrating multiple data sources within the framework of graph-spectrum analysis in order to identify coherent gene subsets.

Results

We investigated several approaches to integrate information derived from different sources that reflect distinct aspects of gene functional relationships including: functional annotations of genes in the form of the Gene Ontology, co-mentioning of genes in the literature, and shared transcription factor binding sites among genes. Given a list of genes, we construct a graph containing the genes in each information space; then the graphs were kernel transformed so they could be integrated; finally functionally coherent subsets were identified using a spectral clustering algorithm. In a series of simulation experiments, known functionally coherent gene sets were mixed and recovered using our approach.

Conclusions

The results indicate that spectral clustering approaches are capable of recovering coherent gene modules even under noisy conditions, and that information integration serves to further enhance this capability. When applied to a real-world data set, our methods revealed biologically sensible modules, and highlighted the importance of information integration. The implementation of the statistical model is provided under the GNU general public license, as an installable Python module, at: http://code.google.com/p/spectralmix.

SUBMITTER: Richards AJ

PROVIDER: S-EPMC3542577 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Publications

Revealing functionally coherent subsets using a spectral clustering and an information integration approach.

Richards Adam J AJ Schwacke John H JH Rohrer Bärbel B Cowart L Ashley LA Lu Xinghua X

BMC systems biology 20121217

<h4>Background</h4>Contemporary high-throughput analyses often produce lengthy lists of genes or proteins. It is desirable to divide the genes into functionally coherent subsets for further investigation, by integrating heterogeneous information regarding the genes. Here we report a principled approach for managing and integrating multiple data sources within the framework of graph-spectrum analysis in order to identify coherent gene subsets.<h4>Results</h4>We investigated several approaches to ...[more]

PMID: 23282411

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Dataset Information

Revealing functionally coherent subsets using a spectral clustering and an information integration approach.

Background

Results

Conclusions

Publications

Revealing functionally coherent subsets using a spectral clustering and an information integration approach.

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