Research Article
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Published Online: 29 May 2013

CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data

Publication: Journal of Computational Biology
Volume 20, Issue Number 6

Abstract

Because a very large number of gene expression data sets are currently publicly available, comparisons across experiments between different laboratories have become a common task. However, most existing methods of comparing gene expression data sets require setting arbitrary cutoffs (e.g., for statistical significance or fold change), which could select genes according to different criteria because of differences in experimental protocols and statistical analysis in different data sets. A new method is proposed for comparing expression profiles across experiments by using the rank of genes in the different datasets. We introduce a maximization statistic, which can be calculated recursively and allows for efficient searches on a large space (paths on a grid). We apply our method to both simulated and real datasets and show that it outperforms other existing rank-based algorithms. CORaL is a novel method for comparison of gene expression data that performs well on simulated and real data. It has the potential for wide and effective use in computational biology.

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Information

Published In

cover image Journal of Computational Biology
Journal of Computational Biology
Volume 20Issue Number 6June 2013
Pages: 433 - 443
PubMed: 23675929

History

Published in print: June 2013
Published online: 29 May 2013
Published ahead of print: 15 May 2013

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Authors

Affiliations

Michael Antosh
Department of Physics, Brown University, Providence, Rhode Island.
Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island.
David Fox
Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island.
Leon N Cooper
Department of Physics, Brown University, Providence, Rhode Island.
Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island.
Nicola Neretti
Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island.
Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island.

Notes

Availability: Source code (Matlab) available at www.sourceforge.net/p/coralv1
Address correspondence to:Dr. Nicola NerettiDepartment of Molecular Biology, Cell Biology, and BiochemistryBrown University70 Ship StreetProvidence, RI 02912E-mail: [email protected]

Author Disclosure Statement

No competing financial interests exist.

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