Open Access Open Badges Methodology article

Randomization techniques for assessing the significance of gene periodicity results

Aleksi Kallio124*, Niko Vuokko24, Markus Ojala24, Niina Haiminen34 and Heikki Mannila24

Author Affiliations

1 Research Environment Services, CSC - IT Center for Science Ltd., P.O. Box 405, Espoo, 02101, Finland

2 Department of Information and Computer Science, Aalto University, P.O. Box 15400, Espoo, 00076, Finland

3 Department of Computer Science, University of Helsinki, P.O. Box 68, Helsinki, 00014, Finland

4 Data Analysis Research Programme, Helsinki Institute for Information Technology HIIT, Helsinki, Finland

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BMC Bioinformatics 2011, 12:330  doi:10.1186/1471-2105-12-330

Published: 9 August 2011



Modern high-throughput measurement technologies such as DNA microarrays and next generation sequencers produce extensive datasets. With large datasets the emphasis has been moving from traditional statistical tests to new data mining methods that are capable of detecting complex patterns, such as clusters, regulatory networks, or time series periodicity. Study of periodic gene expression is an interesting research question that also is a good example of challenges involved in the analysis of high-throughput data in general. Unlike for classical statistical tests, the distribution of test statistic for data mining methods cannot be derived analytically.


We describe the randomization based approach to significance testing, and show how it can be applied to detect periodically expressed genes. We present four randomization methods, three of which have previously been used for gene cycle data. We propose a new method for testing significance of periodicity in gene expression short time series data, such as from gene cycle and circadian clock studies. We argue that the underlying assumptions behind existing significance testing approaches are problematic and some of them unrealistic. We analyze the theoretical properties of the existing and proposed methods, showing how our method can be robustly used to detect genes with exceptionally high periodicity. We also demonstrate the large differences in the number of significant results depending on the chosen randomization methods and parameters of the testing framework.

By reanalyzing gene cycle data from various sources, we show how previous estimates on the number of gene cycle controlled genes are not supported by the data. Our randomization approach combined with widely adopted Benjamini-Hochberg multiple testing method yields better predictive power and produces more accurate null distributions than previous methods.


Existing methods for testing significance of periodic gene expression patterns are simplistic and optimistic. Our testing framework allows strict levels of statistical significance with more realistic underlying assumptions, without losing predictive power. As DNA microarrays have now become mainstream and new high-throughput methods are rapidly being adopted, we argue that not only there will be need for data mining methods capable of coping with immense datasets, but there will also be need for solid methods for significance testing.