Abstract
BackgroundIn 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].ResultsThe 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.ConclusionsDifferent types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.Availabilityhttp://informatics.systemsbiology.net/EPEPT/
Highlights
In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation
In the second and the third settings, ‘Significance Analysis of Microarrays (SAM)’ and ‘Gene Set Enrichment Analysis (GSEA)’, Enhanced P-value Estimator for Permutation Tests (EPEPT) assumes that a gene expression dataset is uploaded
Due to the enormous increase in biological data and in the computational complexity of its analysis, computational biology is shifting towards client-server based computing models
Summary
This section describes the inputs that are expected by EPEPT and the logs and outputs that are generated. File with test statistics and permutation values or a labeled gene expression dataset [required] The file should be a tab delimited text file, a comma separated text file or an Excel file. In the ‘PV’ setting, each column in the file should contain one test statistic and its corresponding permutation values. Outputs The main output of EPEPT is the set of estimated P-values These are reported in a tab delimited text file. Website The website is a simple HTML input form, where the file with the permutation values or labeled dataset can be uploaded and all options can be set using sliders, drop down menus, check boxes and text fields. The results are presented back to the user in the results pane, which depicts the estimated P-values both as text as well as graphically and gives download links for these output files. A stand alone version of EPEPT for MATLAB is included
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