Identifying significantly impacted pathways: a comprehensive review and assessment.

This article provides precise, objective, and reproducible answers to the following important and currently unanswered questions: (i) is there any difference in performance between non-TB and TB methods?, (ii) is there a method that is consistently better than the others in terms of its ability to identify target pathways, accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC)?, (iii) are there any specific pathways that are biased (in the sense of being more likely or less likely to be significant across all methods)?, and (iv) do specific methods have a bias toward specific pathways (e.g., is pathway X likely to be always reported as significant by method Y )?

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