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Open Access Software

EPEPT: A web service for enhanced P-value estimation in permutation tests

Theo A Knijnenburg12*, Jake Lin1, Hector Rovira1, John Boyle1 and Ilya Shmulevich1

Author Affiliations

1 Institute for Systems Biology, Seattle, WA, USA

2 Current Address: Bioinformatics and Statistics, Division of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands

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BMC Bioinformatics 2011, 12:411  doi:10.1186/1471-2105-12-411

Published: 24 October 2011

Abstract

Background

In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1].

Results

The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded.

Conclusions

Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

Availability

http://informatics.systemsbiology.net/EPEPT webcite/