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. 2014 Jul 22;15:622. doi: 10.1186/1471-2164-15-622

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Copyright © 2014 Backes et al.; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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The two distributions represent the result of the column and row I permutation test approach. The original data set revealed a total of 6,226 significantly associated genes (dashed line). Following permutations of the case–control status (red), a significantly decreased number of genes is discovered to be significant. Following the SNP permutations (row permutations I), a significantly increased number of genes was discovered to be significant. The second row based permutation strategy preserved the number of genes (6,226). The respective gene sets have been used as input for the pathway analysis.