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Extra info for A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice
The first variant focuses on the genetic information m weight only. Whenever marker j influences and ranks each edge k ≥ l using the wkl the expression of gene g, the strong correlations between the allelic states of j and other close markers on the genome (caused by genetic linkage) may easily lead to spurious predictions involving neighboring markers. We therefore scanned all markers along the genome and removed all edges that were locally dominated by other edges with the same target. More precisely, for all genes g, we removed any marker i such that there exists another marker j within a window of five markers m > wm .
See also Fig. 1 (continued) 3 A Simple Yet Effective Systems Genetics Inference Approach 39 40 S. Heise et al. to be able to assess the overall effects of the two major pruning steps within our approach (G2 → G4: selection of one candidate edge per eQTL; G4 → G5: removal of edges that most likely stem from indirect effects (TRANSWESD); see Fig. 1). We will mainly focus on the AUPR measure since this is the most appropriate one for sparse networks. 1). The second (TRANSWESD) pruning step achieves a significant (but compared to the eQTL pruning lower) AUPR improvement when using the larger population size, whereas only a minor or even no effect can be seen for reconstruction based on the small population with 300 individuals.
However, one can observe that in the case of low sample size (300) the optimal AUROC/AUPR region is more confined. Thus, the method seems to be fairly robust against a variation of thresholds but an appropriate threshold selection strategy is important for small sample sizes. Generally, the genotype–phenotype threshold t QT for edge detection in G1 seems more sensitive and important than the linkage analysis threshold dmin required in preprocessing. Regarding sensitivity of the performance evaluation, AUROC is much less sensitive to the parameters t QT and dmin than AUPR.