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Fig. 6 | Genome Biology

Fig. 6

From: Identifying significantly impacted pathways: a comprehensive review and assessment

Fig. 6

The number of biased pathways calculated based on Pearson’s moment coefficient. Under the true null hypothesis, an ideal method would produce a uniform distribution of p values from 0 to 1 for every pathway. Here, thresholds of Pearson’s moment coefficient of 0.1 and − 0.1 are used to determine if the empirical distribution of p values is biased toward 0 or 1, respectively. a The total number of biased pathways (toward either 0 or 1) produced by each method. Each method, except GSEA, has at least 66 biased pathways. b The number of pathways biased toward 0 (false positives) produced by different methods. FE produces the highest number (137 out of 150 pathways) of false positives, followed by WRS (114 out of 150) and CePaGSA (112 out of 186). c The number of pathways biased toward 1 (false negatives) produced by different methods. PathNet produces the highest number (129 out of 130) of false negative pathways. The methods in red are TB methods. The methods in blue are non-TB methods

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