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Using Semantic Similarities and csbl.go for Analyzing Microarray Data

  • Kristian OvaskaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1375)

Abstract

Cellular phenotypes result from the combined effect of multiple genes, and high-throughput techniques such as DNA microarrays and deep sequencing allow monitoring this genomic complexity. The large scale of the resulting data, however, creates challenges for interpreting results, as primary analysis often yields hundreds of genes. Gene Ontology (GO), a controlled vocabulary for gene products, enables semantic analysis of such gene sets. GO can be used to define semantic similarity between genes, which enables semantic clustering to reduce the complexity of a result set. Here, we describe how to compute semantic similarities and perform GO-based gene clustering using csbl.go, an R package for GO semantic similarity. We demonstrate the approach with expression profiles from breast cancer.

Keywords

Gene ontology Semantic similarity Measure Hierarchical clustering Expression microarray Data analysis 

Notes

Acknowledgements

I thank Tiia Pelkonen for proofreading.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.University of HelsinkiHelsinkiFinland

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